JAL-2738 unit test for reverse strand gene

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 44e8e16..6b1eb0d 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -337,8 +337,7 @@ public class VCFLoader
     }
 
     StringBuilder sb = new StringBuilder();
-    sb.append(forwardStrand ? reference : Dna
-            .getComplement((char) reference[0]));
+    sb.append(forwardStrand ? (char) reference[0] : complement(reference));
 
     /*
      * inspect alleles and record SNP variants (as the variant
@@ -354,8 +353,8 @@ public class VCFLoader
         if (alleleBase.length == 1)
         {
           sb.append(",").append(
-                  forwardStrand ? alleleBase : Dna
-                          .getComplement((char) alleleBase[0]));
+                  forwardStrand ? (char) alleleBase[0]
+                          : complement(alleleBase));
         }
       }
     }
@@ -377,6 +376,18 @@ public class VCFLoader
   }
 
   /**
+   * A convenience method to complement a dna base and return the string value
+   * of its complement
+   * 
+   * @param reference
+   * @return
+   */
+  protected String complement(byte[] reference)
+  {
+    return String.valueOf(Dna.getComplement((char) reference[0]));
+  }
+
+  /**
    * Determines the location of the query range (chromosome positions) in a
    * different reference assembly.
    * <p>