Add a method to conditionally apply a Consumer on a nullable input

src/main/java/htsjdk/samtools/util/CodeUtil.java

@@ -1,14 +1,66 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2019 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
 package htsjdk.samtools.util;
 
+import java.util.function.Consumer;
+
 /**
  * Miscellaneous util methods that don't fit anywhere else.
  */
 public class CodeUtil {
 
-    /** Mimic of Oracle's nvl() - returns the first value if not null, otherwise the second value. */
+    /**
+     * Mimic of Oracle's nvl() - returns the first value if not null, otherwise the second value.
+     */
     public static <T> T getOrElse(final T value1, final T value2) {
-        if (value1 != null) return value1;
-        else return value2;
+        if (value1 != null) {
+            return value1;
+        } else {
+            return value2;
+        }
     }
 
+    /**
+     * Applied the Consumer on the input if the input is not null,
+     * serves as a way to avoid writing:
+     * <code>
+     *     if(input != null){
+     *         action.apply(input);
+     *     }
+     * </code>
+     * and replacing it with
+     * <code>
+     *     applyIfNotNull(input,action);
+     * </code>
+     * @param input a nullable object
+     * @param action a Consumer that will be applied to the input if it isn't null.
+     * @param <T> the type of the input.
+     */
+    public static <T> void applyIfNotNull(final T input, Consumer<T> action) {
+        if (input != null) {
+            action.accept(input);
+        }
+    }
 }

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -30,7 +30,6 @@
 import htsjdk.samtools.seekablestream.SeekableHTTPStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import htsjdk.samtools.util.nio.DeleteOnExitPathHook;
-import htsjdk.tribble.Tribble;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
@@ -68,7 +67,6 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Scanner;

src/test/java/htsjdk/samtools/util/CodeUtilTest.java

@@ -4,6 +4,8 @@
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.util.List;
+
 public class CodeUtilTest extends HtsjdkTest {
 
     @Test
@@ -13,4 +15,19 @@ public void getOrElseTest() {
         Assert.assertEquals(CodeUtil.getOrElse(null, notNull), notNull);
         Assert.assertEquals((Object) CodeUtil.getOrElse(null, null), (Object) null);
     }
+
+    @Test
+    public void applyIfNotNullNegativeTest() {
+        CodeUtil.applyIfNotNull((Object) null, (o) -> Assert.fail("this shouldn't have been called"));
+        CodeUtil.applyIfNotNull((Integer) null, (o) -> Assert.fail("this shouldn't have been called"));
+        CodeUtil.applyIfNotNull((Double) null, (o) -> Assert.fail("this shouldn't have been called"));
+        CodeUtil.applyIfNotNull((String) null, (o) -> Assert.fail("this shouldn't have been called"));
+        CodeUtil.applyIfNotNull((List<Object>) null, (o) -> Assert.fail("this shouldn't have been called"));
+    }
+
+    @Test(expectedExceptions = AssertionError.class)
+    public void applyIfNotNullPositiveTest() {
+        CodeUtil.applyIfNotNull(1, (o) -> Assert.assertNotEquals(o, 1,
+                "Throwing this proves that the method was called with value 1"));
+    }
 }