[Biojava-l] Having problems using biojava regex.

[Mark Schreiber]

Hi -

>From memory everything should be lower case. BioJava always represents DNA
as lowercase and protein as upper case as per convention.

Try that.

- Mark


On 3/15/07, Charles Danko <dankoc at gmail.com> wrote:
>
> 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();
>    }
> }
> }
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