[Biojava-l] Using REstriction Mapper

[mark.schreiber at novartis.com]

Hi -

Looks like you forgot to include the bytecode.jar on your classpath. Take 
a look at these instructions : http://biojava.org/wiki/BioJava:GetStarted

- Mark

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





ashish mittal <mittalashr at yahoo.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/28/2006 12:54 PM

 
        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using REstriction Mapper


Hi all, 

I am trying to use restriction mapper to search for a list of resctriction 
enzymes in a given sequence. Can some one send me some sample code that 
does the same. I tried following and this code gives exception: 
Exception in thread "main" java.lang.NoClassDefFoundError: 
org/biojava/utils/bytecode/CodeException
        at 
org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)
        at 
org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
        at 
org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:52)
        at 
org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:116)
        at 
org.biojava.bio.seq.impl.ViewSequence.<init>(ViewSequence.java:143)
        at 
org.biojava.bio.molbio.RestrictionMapper.annotate(RestrictionMapper.java:115)
        at seed.rs.rsTry.Searcher.search(Searcher.java:91)
        at seed.rs.rsTry.Searcher.main(Searcher.java:101)


CODE: 

public class Searcher {
 
    ThreadPool tPool = new ThreadPool() {
        public void addRequest(Runnable runnable) {
        }
        public void startThreads() {
        }
        public void stopThreads() {
        }
        public void waitForThreads() {
        }
    };
 
    RestrictionMapper mapper = new RestrictionMapper(tPool);
 
 
 
    /** Creates a new instance of Searcher */
    public Searcher() {
    }
 
    public void search(){
 
 
        try {
            RestrictionEnzyme res1 = new 
RestrictionEnzyme("enz1",DNATools.createDNA("agtg"),0,0);
            RestrictionEnzyme res2 = new 
RestrictionEnzyme("enz2",DNATools.createDNA("gatt"),0,0);
            RestrictionEnzyme res3 = new 
RestrictionEnzyme("enz3",DNATools.createDNA("gatg"),0,0);
 
            mapper.addEnzyme(res1);
            mapper.addEnzyme(res2);
            mapper.addEnzyme(res3);
 
        RestrictionEnzymeManager.register(res1,new TreeSet());
        RestrictionEnzymeManager.register(res2,new TreeSet());
        RestrictionEnzymeManager.register(res3,new TreeSet());
 
 
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        } catch (IllegalAlphabetException ex) {
            ex.printStackTrace();
        }
 
        //RestrictionEnzymeManager  resManager = new 
RestrictionEnzymeManager();
 
        try {
 
            Sequence dnaSeq = 
DNATools.createDNASequence("agtgattcgtatcgattcggatggtcattttt","my_dnaseq");
            Sequence newSeq = mapper.annotate(dnaSeq);
 
        } catch (IllegalSymbolException ex) {
            ex.printStackTrace();
        }
    }
 
    public static void main (String args[])
    {
        Searcher searcherObj = new Searcher();
        searcherObj.search();
    }
}



Thanks in Advance. 
Ashish 





 
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