From 9c1dd670f293d8f33de55133397b4cd2d4baf38e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 21 Sep 2016 16:40:07 +0100
Subject: [PATCH] JAL-2214 test for strict Watson-Crick pairing

---
 src/jalview/analysis/Rna.java      |   48 ++++++++++++++++++++++++++++++++++++
 test/jalview/analysis/RnaTest.java |   27 ++++++++++++++++++++
 2 files changed, 75 insertions(+)

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
diff --git a/test/jalview/analysis/RnaTest.java b/test/jalview/analysis/RnaTest.java
index f33525f..f96d2c9 100644
--- a/test/jalview/analysis/RnaTest.java
+++ b/test/jalview/analysis/RnaTest.java
@@ -188,6 +188,33 @@ public class RnaTest
     }
   }
 
+  @Test(groups = { "Functional" })
+  public void testIsCanonicalPair()
+  {
+    String bases = "acgtuACGTU";
+    for (int i = 0; i < bases.length(); i++)
+    {
+      for (int j = 0; j < bases.length(); j++)
+      {
+        char first = bases.charAt(i);
+        char second = bases.charAt(j);
+        boolean result = Rna.isCanonicalPair(first, second);
+        String pair = new String(new char[] { first, second })
+                .toUpperCase();
+        if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
+                || pair.equals("UA") || pair.equals("GC")
+                || pair.equals("CG"))
+        {
+          assertTrue(pair + " should be valid", result);
+        }
+        else
+        {
+          assertFalse(pair + " should be invalid", result);
+        }
+      }
+    }
+  }
+
   /**
    * Tests for isOpeningParenthesis with char or String argument
    */
-- 
1.7.10.2