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
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)