[Biojava-l] Having problems using biojava regex.

[Charles Danko]

Hi,

I'm having problems using the biojava regex classes.

According to my understanding, the code posted below is the simplest
possible example of this class.

However, my output is:
TAG
false
0
TAG

The TAG, TAG part of the output is for pattern.patternAsString() and
occurence.pattern().patternAsString().  As I understand it, both of these
are correct, leading me to believe that both the Pattern and Matcher objects
are being created correctly.  However, occurences.find() = false and
occurences.groupCount() = 0 ... meaning it's not finding any matches!?

Where am I going wrong?

Many thanks!
Charles

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import org.biojava.utils.regex.*;
import java.util.*;
import java.io.*;

public class Ambiguity2 {
  public static void main(String[] args) {
    try {
        FiniteAlphabet IUPAC = DNATools.getDNA();

        // Create pattern using pattern factory.
        Pattern pattern;
        PatternFactory FACTORY = PatternFactory.makeFactory(IUPAC);
        try{
            pattern = FACTORY.compile("TAG");
        } catch(Exception e) {e.printStackTrace(); return;}
        System.out.println(pattern.patternAsString());

        // Variables needed...
        Matcher occurences;

        // Promoter & Element
        Element WorkingElement = new Element("ElementName");
        SymbolList WorkingPromoter = DNATools.createDNA
("TAGAGATAGACGATAGC");

        // Obtain iterator of patterns.
        try {
            occurences = pattern.matcher( WorkingPromoter );
        } catch(Exception e) {e.printStackTrace(); return;}
        System.out.println(occurences.find());
        System.out.println(occurences.groupCount());
        System.out.println(occurences.pattern().patternAsString());
        // Foreach match
        while( occurences.find() ) {
                // Create Occurence object using information from patterns.
            System.out.println("Match: " +"\t"+ WorkingPromoter +"\n"+
occurences.start() +"\t"+ occurences.group().seqString());
        }
    }

    catch (Exception ex) {
      ex.printStackTrace();
    }
  }
}