X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=466e6c6d8e3e97c73ec96fb1986579dac772e684;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=ca3c6d5159308b1ee589d4b7553ec1be6584f40d;hpb=857a40730ad5db87bfc7a381924717a2162c2b81;p=jalview.git
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index ca3c6d5..466e6c6 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,36 +1,99 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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 .
+ * 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 jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
+
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.datamodel.SequenceFeature;
-
public class Rna
{
- static Hashtable pairHash = new Hashtable();
+
+ 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.length; i++)
+ {
+ // System.out.println(closingPars[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(
+ 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
@@ -43,67 +106,99 @@ public class Rna
* @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 Vector GetSimpleBPs(CharSequence line)
+ throws WUSSParseException
{
-
- Vector stack = new Vector();
- Vector pairs = new Vector();
-
+ Hashtable> stacks = new Hashtable>();
+ Vector pairs = new Vector();
int i = 0;
while (i < line.length())
{
char base = line.charAt(i);
- if ((base == '<') || (base == '(') || (base == '{') || (base == '['))
+ if (isOpeningParenthesis(base))
{
- stack.addElement(i);
+ if (!stacks.containsKey(base))
+ {
+ stacks.put(base, new Stack());
+ }
+ stacks.get(base).push(i);
+
}
- else if ((base == '>') || (base == ')') || (base == '}')
- || (base == ']'))
+ else if (isClosingParenthesis(base))
{
- Object temp = stack.lastElement();
- stack.remove(stack.size() - 1);
- pairs.addElement(temp);
- pairs.addElement(i);
- }
+ char opening = matchingOpeningParenthesis(base);
- i++;
- }
+ if (!stacks.containsKey(opening))
+ {
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_unseen_closing_char",
+ new String[] { new StringBuffer(base).toString() }), i);
+ }
- int numpairs = pairs.size() / 2;
- SequenceFeature[] outPairs = new SequenceFeature[numpairs];
+ Stack stack = stacks.get(opening);
+ if (stack.isEmpty())
+ {
+ // error whilst parsing i'th position. pass back
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_closing_char",
+ new String[] { new StringBuffer(base).toString() }), i);
+ }
+ int temp = stack.pop();
- // Convert pairs to array
- for (int p = 0; p < pairs.size(); p += 2)
+ pairs.add(new SimpleBP(temp, i));
+ }
+ i++;
+ }
+ for (char opening : stacks.keySet())
{
- 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,
- end, "");
- //pairHash.put(begin, end);
-
+ Stack 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
+ {
+ 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
+ *
+ * @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);
- }*/
-
+ /*
+ * 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