Use configuration in VariantAnnotatorEngine too

broadinstitute · Jan 18, 2019 · f07cef9 · f07cef9
1 parent ede5aba
commit f07cef9
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Showing 2 changed files with 23 additions and 9 deletions.
diff --git a/...in/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java b/...in/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java
@@ -1,19 +1,17 @@
 package org.broadinstitute.hellbender.tools.walkers.annotator;
 
-import com.google.common.collect.Sets;
 import htsjdk.variant.variantcontext.*;
 import htsjdk.variant.vcf.*;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.broadinstitute.hellbender.engine.*;
 import org.broadinstitute.hellbender.engine.FeatureContext;
+import org.broadinstitute.hellbender.engine.FeatureDataSource;
 import org.broadinstitute.hellbender.engine.FeatureInput;
 import org.broadinstitute.hellbender.engine.ReferenceContext;
 import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;
 import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData;
-import org.broadinstitute.hellbender.utils.ClassUtils;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.genotyper.ReadLikelihoods;
 import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/ClassUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/ClassUtils.java
@@ -49,17 +49,33 @@ public static <T> List<T> makeInstancesOfSubclasses(final Class<? extends T> cla
         final List<T> results = new ArrayList<>(classes.size());
 
         for (final Class<?> found: classes){
-            if (canMakeInstances(found)){
-                try {
-                    results.add((T)found.newInstance());
-                } catch (InstantiationException | IllegalAccessException e) {
-                    throw new GATKException("Problem making an instance of " + found + " Do check that the class has a non-arg constructor", e);
-                }
+            final T instance = (T) makeInstanceOf(found);
+            if (instance != null) {
+                results.add(instance);
             }
         }
         return results;
     }
 
+    /**
+     * Create objects of a concrete class.
+     *
+     * The public no-arg constructor is called to create the objects.
+     *
+     * @param clazz class to be instantiated
+     * @return new object or {@code null} if cannot be instantiated.
+     */
+    public static <T> T makeInstanceOf(final Class<T> clazz) {
+        if (canMakeInstances(clazz)) {
+            try {
+                return clazz.newInstance();
+            } catch (final InstantiationException | IllegalAccessException e) {
+                throw new GATKException("Problem making an instance of " + clazz + " Do check that the class has a non-arg constructor", e);
+            }
+        }
+        return null;
+    }
+
     /**
      * Finds sub-interfaces of the given interface (in the same package) and returns their simple names.
      */