2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 /* Author: Lauren Michelle Lui
22 * Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
23 * Additional Author: Jan Engelhart (2011) - Structure consensus and bug fixing
24 * Additional Author: Anne Menard (2012) - Pseudoknot support and secondary structure consensus
27 package jalview.analysis;
29 import java.util.ArrayList;
30 import java.util.Arrays;
31 import java.util.HashSet;
32 import java.util.Hashtable;
33 import java.util.Stack;
34 import java.util.Vector;
36 import jalview.analysis.SecStrConsensus.SimpleBP;
37 import jalview.datamodel.SequenceFeature;
42 static Hashtable<Integer, Integer> pairHash = new Hashtable();
44 private static final Character[] openingPars =
45 { '(', '[', '{', '<', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J',
46 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
49 private static final Character[] closingPars =
50 { ')', ']', '}', '>', 'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i', 'j',
51 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't', 'u', 'v', 'w', 'x',
54 private static HashSet<Character> openingParsSet = new HashSet<Character>(
55 Arrays.asList(openingPars));
57 private static HashSet<Character> closingParsSet = new HashSet<Character>(
58 Arrays.asList(closingPars));
60 private static Hashtable<Character, Character> closingToOpening = new Hashtable<Character, Character>()
61 // Initializing final data structure
63 private static final long serialVersionUID = 1L;
65 for (int i = 0; i < openingPars.length; i++)
67 System.out.println(closingPars[i] + "->" + openingPars[i]);
68 put(closingPars[i], openingPars[i]);
73 private static boolean isOpeningParenthesis(char c)
75 return openingParsSet.contains(c);
78 private static boolean isClosingParenthesis(char c)
80 return closingParsSet.contains(c);
83 private static char matchingOpeningParenthesis(char closingParenthesis)
84 throws WUSSParseException
86 if (!isClosingParenthesis(closingParenthesis))
88 throw new WUSSParseException(
89 "Querying matching opening parenthesis for non-closing parenthesis character "
90 + closingParenthesis, -1);
93 return closingToOpening.get(closingParenthesis);
97 * Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
98 * positions in "stack" vector. When a close bracket is reached, pair this
99 * with the last element in the "stack" vector and store in "pairs" vector.
100 * Remove last element in the "stack" vector. Continue in this manner until
101 * the whole string is processed.
104 * Secondary structure line of an RNA Stockholm file
105 * @return Array of SequenceFeature; type = RNA helix, begin is open base
106 * pair, end is close base pair
108 public static Vector<SimpleBP> GetSimpleBPs(CharSequence line)
109 throws WUSSParseException
111 System.out.println(line);
112 Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
113 Vector<SimpleBP> pairs = new Vector<SimpleBP>();
115 while (i < line.length())
117 char base = line.charAt(i);
119 if (isOpeningParenthesis(base))
121 if (!stacks.containsKey(base))
123 stacks.put(base, new Stack<Integer>());
125 stacks.get(base).push(i);
128 else if (isClosingParenthesis(base))
131 char opening = matchingOpeningParenthesis(base);
133 if (!stacks.containsKey(opening))
135 throw new WUSSParseException(
136 "Mismatched (unseen) closing character " + base, i);
139 Stack<Integer> stack = stacks.get(opening);
142 // error whilst parsing i'th position. pass back
143 throw new WUSSParseException("Mismatched closing character "
146 int temp = stack.pop();
148 pairs.add(new SimpleBP(temp, i));
152 for (char opening : stacks.keySet())
154 Stack<Integer> stack = stacks.get(opening);
157 throw new WUSSParseException("Mismatched opening character "
158 + opening + " at " + stack.pop(), i);
164 public static SequenceFeature[] GetBasePairs(CharSequence line)
165 throws WUSSParseException
167 Vector<SimpleBP> bps = GetSimpleBPs(line);
168 SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
169 for (int p = 0; p < bps.size(); p++)
171 SimpleBP bp = bps.elementAt(p);
172 outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
178 public static ArrayList<SimpleBP> GetModeleBP(CharSequence line)
179 throws WUSSParseException
181 Vector<SimpleBP> bps = GetSimpleBPs(line);
182 return new ArrayList<SimpleBP>(bps);
186 * Function to get the end position corresponding to a given start position
189 * - start position of a base pair
190 * @return - end position of a base pair
193 * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
194 * Probably extend this to find the start to a given end? //could be done by
195 * putting everything twice to the hash ArrayList<Integer> pair = new
196 * ArrayList<Integer>(); return pairHash.get(indice); }
200 * Figures out which helix each position belongs to and stores the helix
201 * number in the 'featureGroup' member of a SequenceFeature Based off of RALEE
202 * code ralee-helix-map.
205 * Array of SequenceFeature (output from Rna.GetBasePairs)
207 public static void HelixMap(SequenceFeature[] pairs)
210 int helix = 0; // Number of helices/current helix
211 int lastopen = 0; // Position of last open bracket reviewed
212 int lastclose = 9999999; // Position of last close bracket reviewed
213 int i = pairs.length; // Number of pairs
215 int open; // Position of an open bracket under review
216 int close; // Position of a close bracket under review
219 Hashtable helices = new Hashtable(); // Keep track of helix number for each
222 // Go through each base pair and assign positions a helix
223 for (i = 0; i < pairs.length; i++)
226 open = pairs[i].getBegin();
227 close = pairs[i].getEnd();
229 // System.out.println("open " + open + " close " + close);
230 // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
232 // we're moving from right to left based on closing pair
234 * catch things like <<..>>..<<..>> |
236 if (open > lastclose)
242 * catch things like <<..<<..>>..<<..>>>> |
244 j = pairs.length - 1;
247 int popen = pairs[j].getBegin();
249 // System.out.println("j " + j + " popen " + popen + " lastopen "
250 // +lastopen + " open " + open);
251 if ((popen < lastopen) && (popen > open))
253 if (helices.containsValue(popen)
254 && (((Integer) helices.get(popen)) == helix))
268 // Put positions and helix information into the hashtable
269 helices.put(open, helix);
270 helices.put(close, helix);
272 // Record helix as featuregroup
273 pairs[i].setFeatureGroup(Integer.toString(helix));