X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FRna.java;h=9649240bc3b809dffc222199c762dbd5d18a471c;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=f2ef11887a7c1f55d334b0bb89b47a058e61d463;hpb=be415b56e8ce1bc00f5004c64793ce5d0cb17be8;p=jalview.git
diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index f2ef118..9649240 100644
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -1,118 +1,425 @@
-/* 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 ($$Version-Rel$$)
+ * 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 .
+ * 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.Hashtable;
-import java.util.Vector;
-
+import jalview.analysis.SecStrConsensus.SimpleBP;
import jalview.datamodel.SequenceFeature;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Stack;
public class Rna
{
+
+ /**
+ * Answers true if the character is a valid open pair rna secondary structure
+ * symbol. Currently accepts A-Z, ([{<
+ *
+ * @param c
+ * @return
+ */
+ public static boolean isOpeningParenthesis(char c)
+ {
+ return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{'
+ || c == '<');
+ }
+
+ /**
+ * Answers true if the string is a valid open pair rna secondary structure
+ * symbol. Currently accepts A-Z, ([{<
+ *
+ * @param s
+ * @return
+ */
+ public static boolean isOpeningParenthesis(String s)
+ {
+ return s != null && s.length() == 1
+ && isOpeningParenthesis(s.charAt(0));
+ }
+
+ /**
+ * Answers true if the character is a valid close pair rna secondary structure
+ * symbol. Currently accepts a-z, )]}>
+ *
+ * @param c
+ * @return
+ */
+ public static boolean isClosingParenthesis(char c)
+ {
+ return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}'
+ || c == '>');
+ }
+
+ /**
+ * Answers true if the string is a valid close pair rna secondary structure
+ * symbol. Currently accepts a-z, )]}>
+ *
+ * @param s
+ * @return
+ */
+ public static boolean isClosingParenthesis(String s)
+ {
+ return s != null && s.length() == 1
+ && isClosingParenthesis(s.charAt(0));
+ }
+
+ /**
+ * Returns the matching open pair symbol for the given closing symbol.
+ * Currently returns A-Z for a-z, or ([{< for )]}>, or the input symbol if it
+ * is not a valid closing symbol.
+ *
+ * @param c
+ * @return
+ */
+ public static char getMatchingOpeningParenthesis(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ return (char) (c + 'A' - 'a');
+ }
+ switch (c)
+ {
+ case ')':
+ return '(';
+ case ']':
+ return '[';
+ case '}':
+ return '{';
+ case '>':
+ return '<';
+ default:
+ return c;
+ }
+ }
+
/**
* 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.
+ * with the last matching 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. Parse errors are thrown as exceptions
+ * wrapping the error location - position of the first unmatched closing
+ * bracket, or string length if there is an unmatched opening bracket.
*
* @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
+ * @return
+ * @throw {@link WUSSParseException}
*/
- public static SequenceFeature[] GetBasePairs(String line)
+ protected static List getSimpleBPs(CharSequence line)
+ throws WUSSParseException
{
-
- Vector stack = new Vector();
- Vector pairs = new Vector();
-
+ Hashtable> stacks = new Hashtable>();
+ List pairs = new ArrayList();
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 = getMatchingOpeningParenthesis(base);
+
+ if (!stacks.containsKey(opening))
+ {
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_unseen_closing_char", new String[]
+ { String.valueOf(base) }), i);
+ }
+
+ 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[]
+ { String.valueOf(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())
+ {
+ /*
+ * we have an unmatched opening bracket; report error as at
+ * i (length of input string)
+ */
+ throw new WUSSParseException(MessageManager.formatMessage(
+ "exception.mismatched_opening_char", new String[]
+ { String.valueOf(opening), String.valueOf(stack.pop()) }),
+ i);
+ }
+ }
+ return pairs;
+ }
- int numpairs = pairs.size() / 2;
- SequenceFeature[] outPairs = new SequenceFeature[numpairs];
+ /**
+ * 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); }
+ */
- // Convert pairs to array
- for (int p = 0; p < pairs.size(); p += 2)
+ /**
+ * Answers true if the character is a recognised symbol for RNA secondary
+ * structure. Currently accepts a-z, A-Z, ()[]{}<>.
+ *
+ * @param c
+ * @return
+ */
+ public static boolean isRnaSecondaryStructureSymbol(char c)
+ {
+ return isOpeningParenthesis(c) || isClosingParenthesis(c);
+ }
+
+ /**
+ * Answers true if the string is a recognised symbol for RNA secondary
+ * structure. Currently accepts a-z, A-Z, ()[]{}<>.
+ *
+ * @param s
+ * @return
+ */
+ public static boolean isRnaSecondaryStructureSymbol(String s)
+ {
+ return isOpeningParenthesis(s) || isClosingParenthesis(s);
+ }
+
+ /**
+ * Translates a string to RNA secondary structure representation. Returns the
+ * string with any non-SS characters changed to spaces. Accepted characters
+ * are a-z, A-Z, and (){}[]<> brackets.
+ *
+ * @param ssString
+ * @return
+ */
+ public static String getRNASecStrucState(String ssString)
+ {
+ if (ssString == null)
+ {
+ return null;
+ }
+ StringBuilder result = new StringBuilder(ssString.length());
+ for (int i = 0; i < ssString.length(); i++)
+ {
+ char c = ssString.charAt(i);
+ result.append(isRnaSecondaryStructureSymbol(c) ? c : " ");
+ }
+ return result.toString();
+ }
+
+ /**
+ * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
+ * wobble (G:T/U) pair (either way round), else false
+ *
+ * @param first
+ * @param second
+ * @return
+ */
+ public static boolean isCanonicalOrWobblePair(char first, char second)
+ {
+ if (first > 'Z')
{
- 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, "");
+ first -= 32;
+ }
+ if (second > 'Z')
+ {
+ second -= 32;
}
- return outPairs;
+ switch (first)
+ {
+ case 'A':
+ switch (second)
+ {
+ case 'T':
+ case 'U':
+ return true;
+ }
+ break;
+ case 'C':
+ switch (second)
+ {
+ case 'G':
+ return true;
+ }
+ break;
+ case 'T':
+ case 'U':
+ switch (second)
+ {
+ case 'A':
+ case 'G':
+ return true;
+ }
+ break;
+ case 'G':
+ switch (second)
+ {
+ case 'C':
+ case 'T':
+ case 'U':
+ return true;
+ }
+ break;
+ }
+ return false;
}
/**
- * 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.
+ * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
+ * round), else false
*
- * @param pairs
- * Array of SequenceFeature (output from Rna.GetBasePairs)
+ * @param first
+ * @param second
+ * @return
*/
- public static void HelixMap(SequenceFeature[] pairs)
+ public static boolean isCanonicalPair(char first, char second)
{
+ if (first > 'Z')
+ {
+ first -= 32;
+ }
+ if (second > 'Z')
+ {
+ second -= 32;
+ }
+
+ switch (first)
+ {
+ case 'A':
+ switch (second)
+ {
+ case 'T':
+ case 'U':
+ return true;
+ }
+ break;
+ case 'G':
+ switch (second)
+ {
+ case 'C':
+ return true;
+ }
+ break;
+ case 'C':
+ switch (second)
+ {
+ case 'G':
+ return true;
+ }
+ break;
+ case 'T':
+ case 'U':
+ switch (second)
+ {
+ case 'A':
+ return true;
+ }
+ break;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the matching close pair symbol for the given opening symbol.
+ * Currently returns a-z for A-Z, or )]}> for ([{<, or the input symbol if it
+ * is not a valid opening symbol.
+ *
+ * @param c
+ * @return
+ */
+ public static char getMatchingClosingParenthesis(char c)
+ {
+ if ('A' <= c && c <= 'Z')
+ {
+ return (char) (c + 'a' - 'A');
+ }
+ switch (c)
+ {
+ case '(':
+ return ')';
+ case '[':
+ return ']';
+ case '{':
+ return '}';
+ case '<':
+ return '>';
+ default:
+ return c;
+ }
+ }
+
+ public static SequenceFeature[] getHelixMap(CharSequence rnaAnnotation)
+ throws WUSSParseException
+ {
+ List result = new ArrayList();
+
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
+ Map helices = new HashMap();
+ // 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++)
+ List bps = getSimpleBPs(rnaAnnotation);
+ for (SimpleBP basePair : bps)
{
-
- open = pairs[i].getBegin();
- close = pairs[i].getEnd();
+ final int open = basePair.getBP5();
+ final int close = basePair.getBP3();
// System.out.println("open " + open + " close " + close);
// System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
@@ -129,17 +436,17 @@ public class Rna
/*
* catch things like <<..<<..>>..<<..>>>> |
*/
- j = pairs.length - 1;
- while (j >= 0)
+ int j = bps.size();
+ while (--j >= 0)
{
- int popen = pairs[j].getBegin();
+ int popen = bps.get(j).getBP5();
// 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))
+ && ((helices.get(popen)) == helix))
{
continue;
}
@@ -149,8 +456,6 @@ public class Rna
break;
}
}
-
- j -= 1;
}
// Put positions and helix information into the hashtable
@@ -158,11 +463,13 @@ public class Rna
helices.put(close, helix);
// Record helix as featuregroup
- pairs[i].setFeatureGroup(Integer.toString(helix));
+ result.add(new SequenceFeature("RNA helix", "", open, close,
+ String.valueOf(helix)));
lastopen = open;
lastclose = close;
-
}
+
+ return result.toArray(new SequenceFeature[result.size()]);
}
}