import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.Stack;
import java.util.Vector;
import jalview.datamodel.SequenceFeature;
* @return Array of SequenceFeature; type = RNA helix, begin is open base
* pair, end is close base pair
*/
- public static SequenceFeature[] GetBasePairs(String line)
+ public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
{
-
- Vector stack = new Vector();
+ Stack stack = new Stack();
Vector pairs = new Vector();
int i = 0;
{
char base = line.charAt(i);
- if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+ if ((base == '<') || (base == '(') || (base == '{') || (base == '[')|| (base == 'A')|| (base == 'B')|| (base == 'C')|| (base == 'D')|| (base == '1')|| (base == 'F')|| (base == 'G')|| (base == '2')|| (base == 'I')|| (base == 'J')|| (base == 'K')|| (base == 'L')|| (base == 'M')|| (base == 'N')|| (base == 'O')|| (base == 'P')|| (base == 'Q')|| (base == 'R')|| (base == 'S')|| (base == 'T')|| (base == 'U')|| (base == 'V')|| (base == 'W')|| (base == 'X')|| (base == 'Y')|| (base == 'Z'))
{
- stack.addElement(i);
+ stack.push(i);
}
- else if ((base == '>') || (base == ')') || (base == '}')
- || (base == ']'))
+ else if ((base == '>') || (base == ')') || (base == '}')|| (base == ']')|| (base == 'a')|| (base == 'b')|| (base == 'c')|| (base == 'd')|| (base == 'e')|| (base == 'f')|| (base == 'g')|| (base == 'h')|| (base == 'i')|| (base == 'j')|| (base == 'k')|| (base == 'l')|| (base == 'm')|| (base == 'n')|| (base == 'o')|| (base == 'p')|| (base == 'q')|| (base == 'r')|| (base == 's')|| (base == 't')|| (base == 'u')|| (base == 'v')|| (base == 'w')|| (base == 'x')|| (base == 'y')|| (base == 'z'))
+
{
- Object temp = stack.lastElement();
- stack.remove(stack.size() - 1);
+ if (stack.isEmpty())
+ {
+ // error whilst parsing i'th position. pass back
+ throw new WUSSParseException("Mismatched closing bracket", i);
+ }
+ Object temp = stack.pop();
pairs.addElement(temp);
- pairs.addElement(i);
+ pairs.addElement(i);
+ //System.out.println(pairs);
}
i++;
}
}
}
+