import java.util.Arrays;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.List;
import java.util.Stack;
import java.util.Vector;
public class Rna
{
- static Hashtable<Integer, Integer> pairHash = new Hashtable();
+ static Hashtable<Integer, Integer> pairHash = new Hashtable<Integer, Integer>();
private static final Character[] openingPars = { '(', '[', '{', '<', 'A',
'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O',
}
};
- private static boolean isOpeningParenthesis(char c)
+ public static boolean isOpeningParenthesis(char c)
{
return openingParsSet.contains(c);
}
- private static boolean isClosingParenthesis(char c)
+ public static boolean isClosingParenthesis(char c)
{
return closingParsSet.contains(c);
}
throw new WUSSParseException(
MessageManager.formatMessage(
"exception.querying_matching_opening_parenthesis_for_non_closing_parenthesis",
- new String[] { new StringBuffer(closingParenthesis)
- .toString() }), -1);
+ new String[] { String.valueOf(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.
+ * 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 Vector<SimpleBP> GetSimpleBPs(CharSequence line)
+ public static Vector<SimpleBP> getSimpleBPs(CharSequence line)
throws WUSSParseException
{
Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
{
throw new WUSSParseException(MessageManager.formatMessage(
"exception.mismatched_unseen_closing_char",
- new String[] { new StringBuffer(base).toString() }), i);
+ new String[] { String.valueOf(base) }), i);
}
Stack<Integer> stack = stacks.get(opening);
// error whilst parsing i'th position. pass back
throw new WUSSParseException(MessageManager.formatMessage(
"exception.mismatched_closing_char",
- new String[] { new StringBuffer(base).toString() }), i);
+ new String[] { String.valueOf(base) }), i);
}
int temp = stack.pop();
Stack<Integer> 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[] { new StringBuffer(opening).toString(),
- Integer.valueOf(stack.pop()).toString() }), i);
+ new String[] { String.valueOf(opening),
+ String.valueOf(stack.pop()) }), i);
}
}
return pairs;
}
- public static SequenceFeature[] GetBasePairs(CharSequence line)
+ public static SequenceFeature[] getBasePairs(List<SimpleBP> bps)
throws WUSSParseException
{
- Vector<SimpleBP> bps = GetSimpleBPs(line);
SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
for (int p = 0; p < bps.size(); p++)
{
- SimpleBP bp = bps.elementAt(p);
+ SimpleBP bp = bps.get(p);
outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
bp.getBP3(), "");
}
return outPairs;
}
- public static ArrayList<SimpleBP> GetModeleBP(CharSequence line)
+ public static List<SimpleBP> getModeleBP(CharSequence line)
throws WUSSParseException
{
- Vector<SimpleBP> bps = GetSimpleBPs(line);
+ Vector<SimpleBP> bps = getSimpleBPs(line);
return new ArrayList<SimpleBP>(bps);
}
int close; // Position of a close bracket under review
int j; // Counter
- Hashtable helices = new Hashtable(); // Keep track of helix number for each
- // position
+ Hashtable<Integer, Integer> helices = new Hashtable<Integer, Integer>();
+ // 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++)
if ((popen < lastopen) && (popen > open))
{
if (helices.containsValue(popen)
- && (((Integer) helices.get(popen)) == helix))
+ && ((helices.get(popen)) == helix))
{
continue;
}
}
}
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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 canonical (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')
+ {
+ first -= 32;
+ }
+ if (second > 'Z')
+ {
+ second -= 32;
+ }
+
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff