Merge branch 'develop' into task/JAL-2196pdbeProperties

[jalview.git] / src / jalview / analysis / Rna.java

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index e3d999a..89c5c30 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -359,8 +359,8 @@ public class Rna
   }
 
   /**
-   * Answers true if the base-pair is either a canonical (A-T/U, C-G) or a
-   * wobble (G-T/U) pair (either way round), else false
+   * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
+   * wobble (G:T/U) pair (either way round), else false
    * 
    * @param first
    * @param second
@@ -376,7 +376,7 @@ public class Rna
     {
       second -= 32;
     }
-  
+
     switch (first)
     {
     case 'A':
@@ -417,6 +417,62 @@ public class Rna
   }
 
   /**
+   * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
+   * round), else false
+   * 
+   * @param first
+   * @param second
+   * @return
+   */
+  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
    * is not a valid opening symbol.