/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
/* 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 jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Stack;
import java.util.Vector;
-
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.datamodel.SequenceFeature;
-
public class Rna
{
-
- static Hashtable<Integer, Integer> pairHash = new Hashtable();
-
- private static final Character[] openingPars = {'(','[','{','<','A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'};
- private static final Character[] closingPars = {')',']','}','>','a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z'};
-
- private static HashSet<Character> openingParsSet = new HashSet<Character>(Arrays.asList(openingPars));
- private static HashSet<Character> closingParsSet = new HashSet<Character>(Arrays.asList(closingPars));
- private static Hashtable<Character,Character> closingToOpening = new Hashtable<Character,Character>()
+
+ static Hashtable<Integer, Integer> pairHash = new Hashtable();
+
+ private static final Character[] openingPars = { '(', '[', '{', '<', 'A',
+ 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O',
+ 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z' };
+
+ private static final Character[] closingPars = { ')', ']', '}', '>', 'a',
+ 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o',
+ 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x', 'y', 'z' };
+
+ private static HashSet<Character> openingParsSet = new HashSet<Character>(
+ Arrays.asList(openingPars));
+
+ private static HashSet<Character> closingParsSet = new HashSet<Character>(
+ Arrays.asList(closingPars));
+
+ private static Hashtable<Character, Character> closingToOpening = new Hashtable<Character, Character>()
// Initializing final data structure
{
- private static final long serialVersionUID = 1L;
- {
- for(int i=0;i<openingPars.length;i++)
- {
- System.out.println(closingPars[i]+"->"+openingPars[i]);
- put(closingPars[i],openingPars[i]);
- }
- }};
-
+ private static final long serialVersionUID = 1L;
+ {
+ for (int i = 0; i < openingPars.length; i++)
+ {
+ // System.out.println(closingPars[i] + "->" + openingPars[i]);
+ put(closingPars[i], openingPars[i]);
+ }
+ }
+ };
+
private static boolean isOpeningParenthesis(char c)
{
- return openingParsSet.contains(c);
+ return openingParsSet.contains(c);
}
-
+
private static boolean isClosingParenthesis(char c)
{
- return closingParsSet.contains(c);
+ return closingParsSet.contains(c);
}
- private static char matchingOpeningParenthesis(char closingParenthesis) throws WUSSParseException
+ private static char matchingOpeningParenthesis(char closingParenthesis)
+ throws WUSSParseException
{
- if (!isClosingParenthesis(closingParenthesis))
- {
- throw new WUSSParseException("Querying matching opening parenthesis for non-closing parenthesis character "+closingParenthesis, -1);
- }
-
- return closingToOpening.get(closingParenthesis);
+ if (!isClosingParenthesis(closingParenthesis))
+ {
+ throw new WUSSParseException(
+ MessageManager.formatMessage(
+ "exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis",
+ new String[] { new StringBuffer(closingParenthesis)
+ .toString() }), -1);
+ }
+
+ return closingToOpening.get(closingParenthesis);
}
-
+
/**
* 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 Vector<SimpleBP> GetSimpleBPs(CharSequence line) throws WUSSParseException
+ public static Vector<SimpleBP> GetSimpleBPs(CharSequence line)
+ throws WUSSParseException
{
- System.out.println(line);
- Hashtable<Character,Stack<Integer>> stacks = new Hashtable<Character,Stack<Integer>>();
+ Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
Vector<SimpleBP> pairs = new Vector<SimpleBP>();
int i = 0;
while (i < line.length())
{
char base = line.charAt(i);
-
+
if (isOpeningParenthesis(base))
{
- if (!stacks.containsKey(base)){
- stacks.put(base, new Stack<Integer>());
- }
+ if (!stacks.containsKey(base))
+ {
+ stacks.put(base, new Stack<Integer>());
+ }
stacks.get(base).push(i);
-
+
}
else if (isClosingParenthesis(base))
{
-
- char opening = matchingOpeningParenthesis(base);
-
- if (!stacks.containsKey(opening)){
- throw new WUSSParseException("Mismatched (unseen) closing character "+base, i);
- }
-
- Stack<Integer> stack = stacks.get(opening);
+
+ char opening = matchingOpeningParenthesis(base);
+
+ if (!stacks.containsKey(opening))
+ {
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_unseen_closing_char",
+ new String[] { new StringBuffer(base).toString() }), i);
+ }
+
+ Stack<Integer> stack = stacks.get(opening);
if (stack.isEmpty())
{
// error whilst parsing i'th position. pass back
- throw new WUSSParseException("Mismatched closing character "+base, i);
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_closing_char",
+ new String[] { new StringBuffer(base).toString() }), i);
}
int temp = stack.pop();
-
- pairs.add(new SimpleBP(temp,i));
+
+ pairs.add(new SimpleBP(temp, i));
}
i++;
}
- for(char opening: stacks.keySet())
+ for (char opening : stacks.keySet())
{
- Stack<Integer> stack = stacks.get(opening);
- if (!stack.empty())
- {
- throw new WUSSParseException("Mismatched opening character "+opening+" at "+stack.pop(), i);
- }
+ Stack<Integer> stack = stacks.get(opening);
+ if (!stack.empty())
+ {
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_opening_char",
+ new String[] { new StringBuffer(opening).toString(),
+ Integer.valueOf(stack.pop()).toString() }), i);
+ }
}
return pairs;
}
-
- public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
+
+ public static SequenceFeature[] GetBasePairs(CharSequence line)
+ throws WUSSParseException
{
- Vector<SimpleBP> bps = GetSimpleBPs(line);
- SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
+ Vector<SimpleBP> bps = GetSimpleBPs(line);
+ SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
for (int p = 0; p < bps.size(); p++)
{
- SimpleBP bp = bps.elementAt(p);
- outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),bp.getBP3(), "");
+ SimpleBP bp = bps.elementAt(p);
+ outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
+ bp.getBP3(), "");
}
return outPairs;
}
-
-
- public static ArrayList<SimpleBP> GetModeleBP(CharSequence line) throws WUSSParseException
+
+ public static ArrayList<SimpleBP> GetModeleBP(CharSequence line)
+ throws WUSSParseException
{
- Vector<SimpleBP> bps = GetSimpleBPs(line);
- return new ArrayList<SimpleBP>(bps);
+ Vector<SimpleBP> bps = GetSimpleBPs(line);
+ return new ArrayList<SimpleBP>(bps);
}
-
-
+
/**
* 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
}
}
}
-
git://source.jalview.org / jalview.git / blobdiff