/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-
/* Author: Lauren Michelle Lui
* Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
* */
package jalview.analysis;
-import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.Stack;
import java.util.Vector;
import jalview.datamodel.SequenceFeature;
public class Rna
{
- static Hashtable<Integer, Integer> pairHash = new Hashtable();
+ static Hashtable<Integer, Integer> pairHash = new Hashtable();
+
/**
* Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
* positions in "stack" vector. When a close bracket is reached, pair this
* @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
+ 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);
}
i++;
{
int begin = Integer.parseInt(pairs.elementAt(p).toString());
int end = Integer.parseInt(pairs.elementAt(p + 1).toString());
-
- outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
+
+ outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
end, "");
- //pairHash.put(begin, end);
+ // pairHash.put(begin, end);
}
return outPairs;
}
-
-
+
/**
* Function to get the end position corresponding to a given start position
- * @param indice - start position of a base pair
+ *
+ * @param indice
+ * - start position of a base pair
* @return - end position of a base pair
*/
- /*makes no sense at the moment :(
- public int findEnd(int indice){
- //TODO: Probably extend this to find the start to a given end?
- //could be done by putting everything twice to the hash
- ArrayList<Integer> pair = new ArrayList<Integer>();
- return pairHash.get(indice);
- }*/
-
+ /*
+ * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
+ * Probably extend this to find the start to a given end? //could be done by
+ * putting everything twice to the hash ArrayList<Integer> pair = new
+ * ArrayList<Integer>(); return pairHash.get(indice); }
+ */
/**
* Figures out which helix each position belongs to and stores the helix