Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2aa24a1..d0d26b0 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1603,87 +1603,6 @@ public class ResidueProperties
     return ss.toString();
   }
 
-  /**
-   * Used by getRNASecStrucState
-   * 
-   */
-  public static Hashtable<String, String> toRNAssState;
-
-  public static boolean RNAcloseParen[] = new boolean[255];
-  static
-  {
-    toRNAssState = new Hashtable<String, String>();
-    toRNAssState.put(")", "(");
-    toRNAssState.put("(", "(");
-    toRNAssState.put("]", "[");
-    toRNAssState.put("[", "[");
-    toRNAssState.put("{", "{");
-    toRNAssState.put("}", "{");
-    toRNAssState.put(">", ">");
-    toRNAssState.put("<", ">");
-    toRNAssState.put("A", "A");
-    toRNAssState.put("a", "A");
-    toRNAssState.put("B", "B");
-    toRNAssState.put("b", "B");
-    toRNAssState.put("C", "C");
-    toRNAssState.put("c", "C");
-    toRNAssState.put("D", "D");
-    toRNAssState.put("d", "D");
-    toRNAssState.put("E", "E");
-    toRNAssState.put("e", "E");
-    toRNAssState.put("F", "F");
-    toRNAssState.put("f", "F");
-    toRNAssState.put("G", "G");
-    toRNAssState.put("g", "G");
-    toRNAssState.put("H", "H");
-    toRNAssState.put("h", "H");
-    toRNAssState.put("I", "I");
-    toRNAssState.put("i", "I");
-    toRNAssState.put("J", "J");
-    toRNAssState.put("j", "J");
-    toRNAssState.put("K", "K");
-    toRNAssState.put("k", "K");
-    toRNAssState.put("L", "L");
-    toRNAssState.put("l", "L");
-    toRNAssState.put("M", "M");
-    toRNAssState.put("m", "M");
-    toRNAssState.put("N", "N");
-    toRNAssState.put("n", "N");
-    toRNAssState.put("O", "O");
-    toRNAssState.put("o", "O");
-    toRNAssState.put("P", "P");
-    toRNAssState.put("p", "P");
-    toRNAssState.put("Q", "Q");
-    toRNAssState.put("q", "Q");
-    toRNAssState.put("R", "R");
-    toRNAssState.put("r", "R");
-    toRNAssState.put("S", "S");
-    toRNAssState.put("s", "S");
-    toRNAssState.put("T", "T");
-    toRNAssState.put("t", "T");
-    toRNAssState.put("U", "U");
-    toRNAssState.put("u", "U");
-    toRNAssState.put("V", "V");
-    toRNAssState.put("v", "V");
-    toRNAssState.put("W", "W");
-    toRNAssState.put("w", "W");
-    toRNAssState.put("X", "X");
-    toRNAssState.put("x", "X");
-    toRNAssState.put("Y", "Y");
-    toRNAssState.put("y", "Y");
-    toRNAssState.put("Z", "Z");
-    toRNAssState.put("z", "Z");
-    for (int p = 0; p < RNAcloseParen.length; p++)
-    {
-      RNAcloseParen[p] = false;
-    }
-    for (String k : toRNAssState.keySet())
-    {
-      RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k)
-              .charAt(0);
-    }
-  }
-
   static
   {
     modifications.put("MSE", "MET"); // Selenomethionine
@@ -3008,40 +2927,6 @@ public class ResidueProperties
     return canonical == null ? aa : canonical;
   }
 
-  /**
-   * translate to RNA secondary structure representation
-   * 
-   * @param ssstring
-   * @return ssstring as a RNA-state secondary structure assignment.
-   */
-  public static String getRNASecStrucState(String ssstring)
-  {
-    if (ssstring == null)
-    {
-      return null;
-    }
-    StringBuffer ss = new StringBuffer();
-    for (int i = 0; i < ssstring.length(); i++)
-    {
-      String ssc = ssstring.substring(i, i + 1);
-      if (toRNAssState.containsKey(ssc))
-      {
-        // valid ss character - so return it
-        ss.append(ssc); // (String) toRNAssState.get(ssc));
-      }
-      else
-      {
-        ss.append(" ");
-      }
-    }
-    return ss.toString();
-  }
-
-  public static boolean isCloseParenRNA(char dc)
-  {
-    return RNAcloseParen[dc];
-  }
-
   // main method generates perl representation of residue property hash
   // / cut here
   public static void main(String[] args)