Extracting conditional methods for better readability

broadinstitute · Apr 7, 2023 · 50e9439 · 50e9439
1 parent f691e4b
commit 50e9439
Showing 1 changed file with 10 additions and 2 deletions.
diff --git a/src/main/java/picard/illumina/MarkIlluminaAdapters.java b/src/main/java/picard/illumina/MarkIlluminaAdapters.java
@@ -140,13 +140,17 @@ public class MarkIlluminaAdapters extends CommandLineProgram {
 
     @Override
     protected String[] customCommandLineValidation() {
-        if ((FIVE_PRIME_ADAPTER != null && THREE_PRIME_ADAPTER == null) || (THREE_PRIME_ADAPTER != null && FIVE_PRIME_ADAPTER == null)) {
+        if (hasEitherAdapter()) {
             return new String[]{"THREE_PRIME_ADAPTER and FIVE_PRIME_ADAPTER must either both be null or both be set."};
         } else {
             return null;
         }
     }
 
+    private boolean hasEitherAdapter() {
+        return (FIVE_PRIME_ADAPTER != null && THREE_PRIME_ADAPTER == null) || (THREE_PRIME_ADAPTER != null && FIVE_PRIME_ADAPTER == null);
+    }
+
     @Override
     protected int doWork() {
         IOUtil.assertFileIsReadable(INPUT);
@@ -167,7 +171,7 @@ protected int doWork() {
         {
             final List<AdapterPair> tmp = new ArrayList<AdapterPair>();
             tmp.addAll(ADAPTERS);
-            if (FIVE_PRIME_ADAPTER != null && THREE_PRIME_ADAPTER != null) {
+            if (hasBothAdapters()) {
                 tmp.add(new CustomAdapterPair(FIVE_PRIME_ADAPTER, THREE_PRIME_ADAPTER));
             }
             adapters = tmp.toArray(new AdapterPair[tmp.size()]);
@@ -246,4 +250,8 @@ protected int doWork() {
         CloserUtil.close(in);
         return 0;
     }
+
+    private boolean hasBothAdapters(){
+        return FIVE_PRIME_ADAPTER != null && THREE_PRIME_ADAPTER != null;
+    }
 }