Provide a method in VariantContextWriterBuilder to set an option depe…

…nding on a Boolean. This will allow chaining of the set/unset methods with conditionals.
samtools · Apr 27, 2016 · 4ca1364 · 4ca1364
1 parent f6a7e09
commit 4ca1364
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diff --git a/src/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java b/src/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java
@@ -338,6 +338,16 @@ public VariantContextWriterBuilder unsetOption(final Options option) {
         return this;
     }
 
+    /**
+     * Set or unset option depending on the boolean given
+     * @param option the option to modify
+     * @param setIt true to set the option, false to unset it.
+     * @return this <code>VariantContextWriterBuilder</code>
+     */
+    public VariantContextWriterBuilder modifyOption(final Options option, final boolean setIt) {
+        return (setIt) ? this.setOption(option) : this.unsetOption(option);
+    }
+
     /**
      * Add one option to the set of default <code>Options</code> that will be used as the initial set of options
      * for all VariantContextWriterBuilders created after this call.
@@ -369,6 +379,15 @@ public VariantContextWriterBuilder clearOptions() {
         return this;
     }
 
+    /**
+     * Used for testing; tests if the option is set
+     * @param option the option to test
+     * @return true if the option is set, false otherwise.
+     */
+    boolean isOptionSet(final Options option) {
+        return this.options.contains(option);
+    }
+
     /**
      * Validate and build the <code>VariantContextWriter</code>.
      *

diff --git a/src/tests/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java b/src/tests/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java
@@ -32,6 +32,7 @@
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.util.TabixUtils;
 import htsjdk.variant.VariantBaseTest;
+import htsjdk.variant.variantcontext.writer.Options;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.Test;
@@ -359,4 +360,18 @@ public void testClearOptions() {
         final VariantContextWriterBuilder builder = new VariantContextWriterBuilder().clearOptions();
         Assert.assertTrue(builder.options.isEmpty());
     }
+
+    @Test
+    public void testModifyOption() {
+        final VariantContextWriterBuilder builder = new VariantContextWriterBuilder().clearOptions();
+        for (final Options option : Options.values()) {
+            Assert.assertFalse(builder.isOptionSet(option)); // shouldn't be set
+            builder.modifyOption(option, false);
+            Assert.assertFalse(builder.isOptionSet(option)); // still shouldn't be set
+            builder.modifyOption(option, true);
+            Assert.assertTrue(builder.isOptionSet(option)); // now is set
+            builder.modifyOption(option, false);
+            Assert.assertFalse(builder.isOptionSet(option)); // has been unset
+        }
+    }
 }