Simplify override

broadinstitute · Jun 14, 2019 · c9936e1 · c9936e1
1 parent 8e1f238
commit c9936e1
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Showing 2 changed files with 13 additions and 9 deletions.
diff --git a/.../java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java b/.../java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/EvaluationContext.java
@@ -17,8 +17,8 @@
 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 List<VariantEvaluator> evaluationInstances;
-    private final Set<Class<? extends VariantEvaluator>> evaluationClasses;
+    protected final List<VariantEvaluator> evaluationInstances;
+    protected final Set<Class<? extends VariantEvaluator>> evaluationClasses;
 
     public EvaluationContext(final VariantEval walker, final Set<Class<? extends VariantEvaluator>> evaluationClasses) {
         this(walker, evaluationClasses, true);
@@ -27,24 +27,19 @@ 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 = initializeEvaluationInstances(doInitialize);
-    }
+        this.evaluationInstances = new ArrayList<>(evaluationClasses.size());
 
-    protected List<VariantEvaluator> initializeEvaluationInstances(boolean doInitialize) {
-        List<VariantEvaluator> ret = new ArrayList<>(evaluationClasses.size());
         for ( final Class<? extends VariantEvaluator> c : evaluationClasses ) {
             try {
                 final VariantEvaluator eval = c.newInstance();
                 if ( doInitialize ) eval.initialize(walker);
-                ret.add(eval);
+                evaluationInstances.add(eval);
             } catch (InstantiationException e) {
                 throw new GATKException("Unable to instantiate eval module '" + c.getSimpleName() + "'", e);
             } catch (IllegalAccessException e) {
                 throw new GATKException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e);
             }
         }
-
-        return ret;
     }
 
     /**

diff --git a/...n/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/VariantEvalUtils.java b/...n/java/org/broadinstitute/hellbender/tools/walkers/varianteval/util/VariantEvalUtils.java
@@ -310,4 +310,13 @@ private void addMapping(HashMap<String, Collection<VariantContext>> mappings, St
             mappings.put(sample, new ArrayList<>(1));
         mappings.get(sample).add(vc);
     }
+
+    /**
+     * Returns a map of all detected VariantStratifier classes
+     *
+     * @return An unmodifiable map of all VariantStratifier classes
+     */
+    public static Map<String, Class<? extends VariantStratifier>> getStratifierClasses() {
+        return Collections.unmodifiableMap(stratifierClasses);
+    }
 }