/*
 * Rajarshi Guha <rajarshi@presidency.com>
 * 26/04/2006
 *
 * Uses the ToxTree program developed by 
 * Nina Jeliazkova, IdeaConsult Ltd. Sofia, Bulgaria
 *
 */

import toxTree.tree.*;
import toxTree.core.*;
import toxTree.data.*;

import toxTree.exceptions.DecisionResultException;

import javax.swing.*;
import java.awt.*;
import java.io.*;

import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.interfaces.Molecule;
import org.openscience.cdk.exception.CDKException;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServlet;
import javax.servlet.ServletContext;
import org.apache.axis.MessageContext;
import org.apache.axis.transport.http.HTTPConstants;

public class toxTreeWS  {

    public toxTreeWS() {}

    public String getCramerClass(String smiles) throws CDKException {

        MessageContext mcon = MessageContext.getCurrentContext();
        ServletContext scon = ((HttpServlet)mcon.getProperty(HTTPConstants.MC_HTTP_SERVLET)).getServletContext();
        String baseDir = scon.getRealPath("/") + "WEB-INF/lib";

	//String baseDir = "/usr/local/share/java/tomcat/webapps/tox/WEB-INF/lib";
	Introspection.addDirectory(baseDir);

	ToxTreeModule toxTreeModel = null;
	DecisionMethodsList methods = new DecisionMethodsList();
	try {
	    methods.loadAllFromPlugins();
	} catch (Exception e) {
	    e.printStackTrace();
	}


	ToxTreeData data = new ToxTreeData(null);

	// set up a new molecule to test
	SmilesParser sp = new SmilesParser();
	Molecule m = sp.parseSmiles(smiles);
	m.setProperty("SMILES", "XYZ");
	data.newMolecule(m);

	// prepare to classify
	IDecisionMethod method = methods.getMethod(0);
	IDecisionResult result = method.createDecisionResult();

	// classify!
	try {
	    data.classify(result);
	} catch (DecisionResultException dre) {
	    throw new CDKException(dre.toString());
	}

	// parse the string form of the result

	return(result.getCategory().getName()+"#"+result.getCategory().getExplanation());

    }

    public static void main(String[] args) {
	toxTreeWS tws = new toxTreeWS();
	try {
	    String res = tws.getCramerClass(args[0]);
	    System.out.println(res);
	    System.exit(0);
	} catch (CDKException cdke) {
	    cdke.printStackTrace();
	}
    }

    private HttpServletRequest getRequest() { 
        MessageContext context = MessageContext.getCurrentContext(); 
        HttpServletRequest req = (HttpServletRequest) context.getProperty(HTTPConstants.MC_HTTP_SERVLETREQUEST);
     return req; 
    } 


}