X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FRna.java;h=c5207f7c3aeaf61ba173c6098b1f4d63c007b97a;hb=6235128370382f0fecdf3ba1cc683052c5aa11e7;hp=69a228ba8ac0496fb8f5c42bacdc1f35341fc48a;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 69a228b..c5207f7 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,12 +1,13 @@
-/* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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
@@ -14,20 +15,68 @@
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
-
/* 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
@@ -40,49 +89,89 @@ 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 Vector GetSimpleBPs(CharSequence line) throws WUSSParseException
{
-
- Vector stack = new Vector();
- Vector pairs = new Vector();
-
+ 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 ((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);
+
+ 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++;
}
-
- int numpairs = pairs.size() / 2;
- SequenceFeature[] outPairs = new SequenceFeature[numpairs];
-
- // Convert pairs to array
- for (int p = 0; p < pairs.size(); p += 2)
+ 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, "");
+ 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
@@ -159,7 +248,6 @@ public class Rna
// Record helix as featuregroup
pairs[i].setFeatureGroup(Integer.toString(helix));
- pairs[i].setFeatureGroup(Integer.toString(helix));
lastopen = open;
lastclose = close;
@@ -167,3 +255,4 @@ public class Rna
}
}
}
+