X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=7c077088af2c9ce76661c8e13dcf09c22069f9d9;hb=9c1dd670f293d8f33de55133397b4cd2d4baf38e;hp=e3d999a98e6158e45b80811290a150eb25654662;hpb=4ed0cd5f8477ba52a9f5b19b021f8f6183f9dd61;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index e3d999a..7c07708 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -416,6 +416,54 @@ public class Rna
     return false;
   }
 
+  public static boolean isCanonicalPair(char first, char second)
+  {
+
+    if (first > 'Z')
+    {
+      first -= 32;
+    }
+    if (second > 'Z')
+    {
+      second -= 32;
+    }
+
+    switch (first)
+    {
+    case 'A':
+      switch (second)
+      {
+      case 'T':
+      case 'U':
+        return true;
+      }
+      break;
+    case 'G':
+      switch (second)
+      {
+      case 'C':
+        return true;
+      }
+      break;
+    case 'C':
+      switch (second)
+      {
+      case 'G':
+        return true;
+      }
+      break;
+    case 'T':
+    case 'U':
+      switch (second)
+      {
+      case 'A':
+        return true;
+      }
+      break;
+    }
+    return false;
+  }
+
   /**
    * Returns the matching close pair symbol for the given opening symbol.
    * Currently returns a-z for A-Z, or )]}> for ([{<, or the input symbol if it