X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=e3d999a98e6158e45b80811290a150eb25654662;hb=4ed0cd5f8477ba52a9f5b19b021f8f6183f9dd61;hp=f497f0e4e909be7d49f6930d4d4c8dfe3bf9a532;hpb=32522ec3c4179494249e085506977f21f83e9b2e;p=jalview.git

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index f497f0e..e3d999a 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -52,6 +52,19 @@ public class Rna
   }
 
   /**
+   * Answers true if the string is a valid open pair rna secondary structure
+   * symbol. Currently accepts A-Z, ([{<
+   * 
+   * @param s
+   * @return
+   */
+  public static boolean isOpeningParenthesis(String s)
+  {
+    return s != null && s.length() == 1
+            && isOpeningParenthesis(s.charAt(0));
+  }
+
+  /**
    * Answers true if the character is a valid close pair rna secondary structure
    * symbol. Currently accepts a-z, )]}>
    * 
@@ -64,6 +77,19 @@ public class Rna
   }
 
   /**
+   * Answers true if the string is a valid close pair rna secondary structure
+   * symbol. Currently accepts a-z, )]}>
+   * 
+   * @param s
+   * @return
+   */
+  public static boolean isClosingParenthesis(String s)
+  {
+    return s != null && s.length() == 1
+            && isClosingParenthesis(s.charAt(0));
+  }
+
+  /**
    * Returns the matching open pair symbol for the given closing symbol.
    * Currently returns A-Z for a-z, or ([{< for )]}>, or the input symbol if it
    * is not a valid closing symbol.
@@ -298,6 +324,18 @@ public class Rna
   }
 
   /**
+   * Answers true if the string is a recognised symbol for RNA secondary
+   * structure. Currently accepts a-z, A-Z, ()[]{}<>.
+   * 
+   * @param s
+   * @return
+   */
+  public static boolean isRnaSecondaryStructureSymbol(String s)
+  {
+    return isOpeningParenthesis(s) || isClosingParenthesis(s);
+  }
+
+  /**
    * Translates a string to RNA secondary structure representation. Returns the
    * string with any non-SS characters changed to spaces. Accepted characters
    * are a-z, A-Z, and (){}[]<> brackets.