/*
 * Updated 01/03/06 to use the latest CDK QSAR package
 *
 */
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.qsar.*;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.io.CMLWriter;
import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.io.listener.PropertiesListener;
import org.openscience.cdk.qsar.result.*;

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;

import java.util.*;
import java.io.*;


public class CDKdesc {
    PropertiesListener propsListener;
    public CDKdesc() {};
    public String getDescriptors(String moleculeString, String classes) throws CDKException {

        DescriptorEngine de = null;

        // Convert the String representation to a Molecule
        StringReader reader = new StringReader(moleculeString);
        MDLReader mdlr = new MDLReader(reader);
        IChemFile chemFile = (IChemFile) mdlr.read((IChemObject)new ChemFile());
        IChemSequence chemSequence = chemFile.getChemSequence(0);
        IChemModel chemModel = chemSequence.getChemModel(0);
        IMolecule molecule = chemModel.getSetOfMolecules().getMolecule(0);

	// we need to get the real path corresponding to "/", for this service
	// given that we can then get a list of the CDK jars so that we can 
	// examine them for Descriptor classes in the constructor of DescriptorEngine
	MessageContext mcon = MessageContext.getCurrentContext();
	ServletContext scon = ((HttpServlet)mcon.getProperty(HTTPConstants.MC_HTTP_SERVLET)).getServletContext();
	String baseDir = scon.getRealPath("/") + "WEB-INF/lib";
	File file = new File(baseDir);
	String[] jars = file.list();
	if (jars == null || jars.length == 0) {
	    System.out.println("No jars found for this web app");
	} else {
	    for (int i = 0; i < jars.length; i++) {
		jars[i] = baseDir+"/"+jars[i]; // make the paths fully qualified
	    }
	}

	de = new DescriptorEngine(DescriptorEngine.MOLECULAR, jars);
	HashMap<String, Object> map = new HashMap<String, Object>();

        if (classes.equalsIgnoreCase("all")) {
	    classes = "topological,geometrical,constitutional,electronic,hybrid";
        } 

	// split the comma seperated list 
	String[] classlist = classes.split(",");
	List deInstances = de.getDescriptorInstances();
	for (Object o : deInstances) {
	    IDescriptor desc = (IDescriptor)o;
	    DescriptorSpecification spec = desc.getSpecification();

	    String[] comps = spec.getSpecificationReference().split("#");
	    String descName = comps[1];

	    String[] descClasses = de.getDictionaryClass(spec);
	    if (descClasses == null) {
		continue;
	    }
		
	    // see if the class matches any of our specified classes
	    boolean matches = false;
	    for (String s1 : descClasses) {
		for (String s2 : classlist) {
		    if (s1.equals(s2+"Descriptor")) {
			matches = true;
			break;
		    }
		}
		if (matches) break;
	    }
	    if (!matches) continue;
	    try {
		DescriptorValue value = desc.calculate(molecule);
		IDescriptorResult result = value.getValue();
		    
		if (result instanceof DoubleResult) {
		    molecule.setProperty(descName, ((DoubleResult) result).doubleValue());
		    map.put(descName, ((DoubleResult) result).doubleValue());
		} else if (result instanceof IntegerResult) {
		    molecule.setProperty(descName, ((IntegerResult) result).intValue());
		    map.put(descName, ((IntegerResult) result).intValue());
		} else if (result instanceof DoubleArrayResult) {
		    for (int i = 0; i < ((DoubleArrayResult) result).size(); i++) {
			molecule.setProperty(descName + "." + i, ((DoubleArrayResult) result).get(i));
			map.put(descName + "." + i, ((DoubleArrayResult) result).get(i));
		    }
		} else if (result instanceof IntegerArrayResult) {
		    for (int i = 0; i < ((IntegerArrayResult) result).size(); i++){
			molecule.setProperty(descName + "." + i, ((IntegerArrayResult) result).get(i));
			map.put(descName + "." + i, ((IntegerArrayResult) result).get(i));
		    }
		}
	    } catch (CDKException e) {
		throw new CDKException(e.toString());
	    }
	}
	
	StringWriter writer = new StringWriter();
        try {
	    MDLWriter mdlwriter = new MDLWriter(writer);
	    mdlwriter.setSdFields(map);
	    mdlwriter.write(molecule);
	    mdlwriter.close();
	} catch (Exception e) {
	    throw new CDKException(e.toString());
	}
        return(writer.toString());        
    }

    private static String readFile(String inFileName) throws IOException {
        FileReader r = null;
        try {
            r = new FileReader(new File(inFileName));
            StringBuffer sb = new StringBuffer();
            char[] b = new char[8192];
            int n;
            while ((n = r.read(b)) > 0) { sb.append(b, 0, n); }
            return sb.toString();
        } finally {
            try {
                r.close();
            } catch (IOException e1) {
                e1.printStackTrace();
            }
        }
    }    
    
}