/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
* Copyright (C) 2014 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.
*
* 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 .
* 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/
* Additional Author: Jan Engelhart (2011) - Structure consensus and bug fixing
* Additional Author: Anne Menard (2012) - Pseudoknot support and secondary structure consensus
* */
package jalview.analysis;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Stack;
import java.util.Vector;
import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.SequenceFeature;
public class Rna
{
static Hashtable 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 openingParsSet = new HashSet(Arrays.asList(openingPars));
private static HashSet closingParsSet = new HashSet(Arrays.asList(closingPars));
private static Hashtable closingToOpening = new Hashtable()
// Initializing final data structure
{
private static final long serialVersionUID = 1L;
{
for(int i=0;i"+openingPars[i]);
put(closingPars[i],openingPars[i]);
}
}};
private static boolean isOpeningParenthesis(char c)
{
return openingParsSet.contains(c);
}
private static boolean isClosingParenthesis(char c)
{
return closingParsSet.contains(c);
}
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);
}
/**
* 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
* with the last element in the "stack" vector and store in "pairs" vector.
* Remove last element in the "stack" vector. Continue in this manner until
* the whole string is processed.
*
* @param line
* Secondary structure line of an RNA Stockholm file
* @return Array of SequenceFeature; type = RNA helix, begin is open base
* pair, end is close base pair
*/
public static Vector GetSimpleBPs(CharSequence line) throws WUSSParseException
{
System.out.println(line);
Hashtable> stacks = new Hashtable>();
Vector pairs = new Vector();
int i = 0;
while (i < line.length())
{
char base = line.charAt(i);
if (isOpeningParenthesis(base))
{
if (!stacks.containsKey(base)){
stacks.put(base, new Stack());
}
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 stack = stacks.get(opening);
if (stack.isEmpty())
{
// error whilst parsing i'th position. pass back
throw new WUSSParseException("Mismatched closing character "+base, i);
}
int temp = stack.pop();
pairs.add(new SimpleBP(temp,i));
}
i++;
}
for(char opening: stacks.keySet())
{
Stack stack = stacks.get(opening);
if (!stack.empty())
{
throw new WUSSParseException("Mismatched opening character "+opening+" at "+stack.pop(), i);
}
}
return pairs;
}
public static SequenceFeature[] GetBasePairs(CharSequence line) throws WUSSParseException
{
Vector 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(), "");
}
return outPairs;
}
public static ArrayList GetModeleBP(CharSequence line) throws WUSSParseException
{
Vector bps = GetSimpleBPs(line);
return new ArrayList(bps);
}
/**
* Function to get the end position corresponding to a given start position
* @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 pair = new ArrayList();
return pairHash.get(indice);
}*/
/**
* Figures out which helix each position belongs to and stores the helix
* number in the 'featureGroup' member of a SequenceFeature Based off of RALEE
* code ralee-helix-map.
*
* @param pairs
* Array of SequenceFeature (output from Rna.GetBasePairs)
*/
public static void HelixMap(SequenceFeature[] pairs)
{
int helix = 0; // Number of helices/current helix
int lastopen = 0; // Position of last open bracket reviewed
int lastclose = 9999999; // Position of last close bracket reviewed
int i = pairs.length; // Number of pairs
int open; // Position of an open bracket under review
int close; // Position of a close bracket under review
int j; // Counter
Hashtable helices = new Hashtable(); // Keep track of helix number for each
// position
// Go through each base pair and assign positions a helix
for (i = 0; i < pairs.length; i++)
{
open = pairs[i].getBegin();
close = pairs[i].getEnd();
// System.out.println("open " + open + " close " + close);
// System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
// we're moving from right to left based on closing pair
/*
* catch things like <<..>>..<<..>> |
*/
if (open > lastclose)
{
helix++;
}
/*
* catch things like <<..<<..>>..<<..>>>> |
*/
j = pairs.length - 1;
while (j >= 0)
{
int popen = pairs[j].getBegin();
// System.out.println("j " + j + " popen " + popen + " lastopen "
// +lastopen + " open " + open);
if ((popen < lastopen) && (popen > open))
{
if (helices.containsValue(popen)
&& (((Integer) helices.get(popen)) == helix))
{
continue;
}
else
{
helix++;
break;
}
}
j -= 1;
}
// Put positions and helix information into the hashtable
helices.put(open, helix);
helices.put(close, helix);
// Record helix as featuregroup
pairs[i].setFeatureGroup(Integer.toString(helix));
lastopen = open;
lastclose = close;
}
}
}