X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FDna.java;fp=src%2Fjalview%2Fanalysis%2FDna.java;h=2ad8487bcdec37ef0e84d4e83d68f1e573663155;hb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;hp=d534c8f52e1592cc5d5e9b8ae059358540814844;hpb=a2703f9c2948fba9747b304fed02b7bbc5d32b37;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index d534c8f..2ad8487 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -437,6 +437,7 @@ public class Dna
   {
     List<int[]> skip = new ArrayList<>();
     int[] skipint = null;
+
     int npos = 0;
     int vc = 0;
 
@@ -574,7 +575,7 @@ public class Dna
             skip.add(skipint);
             skipint = null;
           }
-          if (aa.equals("STOP"))
+          if (aa.equals(ResidueProperties.STOP))
           {
             aa = STOP_ASTERIX;
           }
@@ -881,6 +882,23 @@ public class Dna
   }
 
   /**
+   * Answers the reverse complement of the input string
+   * 
+   * @see #getComplement(char)
+   * @param s
+   * @return
+   */
+  public static String reverseComplement(String s)
+  {
+    StringBuilder sb = new StringBuilder(s.length());
+    for (int i = s.length() - 1; i >= 0; i--)
+    {
+      sb.append(Dna.getComplement(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /**
    * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
    * are treated as on http://reverse-complement.com/. Anything else is left
    * unchanged.