[Biojava-l] pdbtoXML in Linux and JRE,SE

[jon portuondo murguiondo]

Hello,
I have a problem in the application PDBtoXML.java (I work in Linux). I have the Java 
(TM) 2 Runtime Environment, Standard Edition (v 1.4.1). I have the biojava libraries 
biojava-20020823.jar, bytecode-0.91.jar, jakarta-regexp.jar, xerces.jar in the 
CLASSPATH environment variable.
This is the error:

[jon@diana ~]$ java pdbtoXML.java 1FS1.pdb
Exception in thread "main" java.lang.NoClassDefFoundError: pdbtoXML/java

This is the script of pdbtoXML.java:

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.bio.program;

import org.xml.sax.ContentHandler;
import org.xml.sax.XMLReader;
import org.xml.sax.SAXException;
import java.util.*;

import org.biojava.bio.program.sax.PdbSAXParser;
import org.biojava.bio.program.xml.SimpleXMLEmitter;

/**
 * <p>
 * A class that converts Protein Data Bank (PDB) to
 * XML that will validate against the biojava:MacromolecularStructure DTD.
 * <p>
 * <b>Note this code is experimental and subject to change without notice.
 * </b>
 * <p>
 * Copyright &copy; 2000 Cambridge Antibody Technology.
 * All Rights Reserved.
 * <p>
 * Primary author -<ul>
 * <li>Simon Brocklehurst (CAT)
 * </ul>
 * Other authors  -<ul>
 * <li>Tim Dilks          (CAT)
 * <li>Colin Hardman      (CAT)
 * <li>Stuart Johnston    (CAT)
 *</ul>
 *
 * This code was first released to the biojava.org project, July 2000.
 *
 * @author Cambridge Antibody Technology (CAT)
 * @version 0.1
 * 
 * @see org.biojava.bio.program.sax.BlastLikeSAXParser
 * @see SimpleXMLEmitter
 */
public class PdbToXMLConverter {

    private String            oInput;
    private XMLReader         oParser;
    private boolean           tStrict         = true;

    /**
     * Creates a new <code>BlastToXMLConverter</code> instance.
     *
     */
    public PdbToXMLConverter(String poInput) {
        oInput = poInput;
    }

    public void convert() throws java.io.IOException,
                                 org.xml.sax.SAXException {

        //Access functionality of biojava classes through
        //standard org.xml.sax interfaces...

        /**
         * Create a SAX Parser that takes the native output
         * from blast-like bioinformatics software.
         */
        oParser = (XMLReader) new PdbSAXParser();


        /**
         * Dynamically change configuration of the parser
         * in regard of Namespace support. Here,
         * the xml.org/features/namespaces feature is simply "reset"
         * to its default value for SAX2.
         * The xml.org/features/namespaces-prefixes feature is
         * also set to true.  This is to ensure that xmlns attributes
         * are reported by the parser. These are required because we want
         * to configure the XMLEmitter to output qualified names (see below).
         */
        try {
            oParser.setFeature("http://xml.org/sax/features/namespaces",true);
            oParser.setFeature("http://xml.org/sax/features/namespace-prefixes";,
                               true);

        } catch (Exception e) {
            //If an illegal conmbination of features is chosen,
            //roll back to default settings. Output a warning,
            //even though this might mess up the output...
            System.out.println("WARNING: ignoring attempt to set illegal " +
                               "combination of parser features");
        }
        /**
         * Create an XML ContentHandler. This
         * implementation of the DocumentHandler
         * interface simple outputs nicely formatted
         * XML. Passing a true value to the SimpleXMLEmitter
         * constructor instructs the ContentHandler
         * to take QNames from the SAXParser, rather
         * than LocalNames.
         */
        ContentHandler oHandler  = 
            (ContentHandler) new SimpleXMLEmitter(true);

        /**
         * Give the parser a reference to the ContentHandler
         * so that it can send SAX2 mesagges.
         */
        oParser.setContentHandler(oHandler);
        /**
         * Now make the Parser parse the output from the
         * blast-like software and emit XML as specificed
         * by the DocumentHandler.
         */
        oParser.parse(oInput);  

        System.out.println();
        
    }

}

I would be pleased you could help to solve my problem. Thank you. 
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