import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.rmi.RemoteException;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Set;

import javax.xml.namespace.QName;
import javax.xml.rpc.ServiceException;

import org.apache.axis.AxisFault;
import org.apache.axis.client.Call;
import org.apache.axis.client.Service;
import org.w3c.dom.Element;

public class ClustalWCOrig {

    public static void main(String[] args) {

        try {

            final String server = "http://bibiwsserv.techfak.uni-bielefeld.de";
            final URL wsdl = new URL("http://bibiserv.techfak.uni-bielefeld.de/wsdl/ClustalW.wsdl");
            //final String server = "http://bibiwstest.techfak.uni-bielefeld.de";
            //final URL wsdl = new URL("http://bibiwstest.techfak.uni-bielefeld.de/ClustalW/axis/ClustalWPort?wsdl");
            
            // parameter to hashtable
            Hashtable paramshash = parseParameter(args);

            if (!paramshash.containsKey("F")) {
                System.err.println("java "+ClustalWCOrig.class.getSimpleName()+" -F <sequenceML File>\n\t[-MATRIX (BLOSUM|PAM|GONNET|ID|WUERZBURG)]\n\t[-GAPOPEN <INT>]\n\t[-GAPEXT <INT>");
                System.exit(0);
            }

            // read sequence from file
            File infile = new File((String) paramshash.get("F"));
            BufferedReader reader = new BufferedReader(new FileReader(infile));
            String line;
            StringBuffer sequence = new StringBuffer();
            while ((line = reader.readLine()) != null) {
                sequence.append(line + "\n");
            }
            reader.close();

            // remove File parameter
            paramshash.remove("F");

        

            // prepare the call (the same for all called methods)
            Service ser = new Service(wsdl, new QName(
                    server+"/ClustalW/axis/ClustalWPort",
                    
                    "ClustalWImplementationService"));
            Call call = (Call) ser.createCall(new QName("ClustalWPort"), "request_orig");
            // call and get id
            String id = (String) call.invoke(new Object[] {hashtable2array(paramshash), sequence.toString() });
            // print id on STDOUT
            System.err.println("get id - '" + id + "'");
            int statuscode = 601;
            while ((statuscode > 600) && (statuscode < 700)) {
                try {
                    Thread.sleep(2500);
                    call = (Call) ser.createCall(new QName("ClustalWPort"), "response_orig");
                    // call and get result as DOM Tree(if finished)
                    String result = (String) call.invoke(new Object[] { id });

                    // and print it to STDOUT
                    System.out.println(result);
                    
                    // finished
                    statuscode = 600;
                } catch (InterruptedException e) {
                    System.err.println("process can't sleep!");
                } catch (RemoteException e) {
                    // on error WS will throw a soapfault as hobitstatuscode
                    Element root = ((AxisFault) e).lookupFaultDetail(new QName(
                            "http://hobit.sourceforge.net/xsds/hobitStatuscode.xsd", "hobitStatuscode"));
                    if (root == null) {
                        System.err.println("ws remote error (no Hobitstatuscode): " + e.toString());
                        System.exit(1);
                    }
                    String description = root.getLastChild().getFirstChild().getNodeValue();
                    statuscode = Integer.parseInt(root.getFirstChild().getFirstChild().getNodeValue());
                    // print Statusinformation to STDERR
                    System.err.println("(" + statuscode + " - " + description + ")");
                }
            }

            // error handling with proper information for the user

        } catch (RemoteException e) {
            // on error WS will throw a soapfault as hobitstatuscode
            Element root = ((AxisFault) e).lookupFaultDetail(new QName(
                    "http://hobit.sourceforge.net/xsds/hobitStatuscode.xsd", "hobitStatuscode"));
            if (root == null) {
                System.err.println("ws remote error (no Hobitstatuscode): " + e.toString());
                System.exit(1);
            }
            String description = root.getLastChild().getFirstChild().getNodeValue();
            String code = root.getFirstChild().getFirstChild().getNodeValue();
            System.out.println("Statuscode:  " + code);
            System.out.println("Description: " + description);
            /*
             * Using this kind of Webservice there is only one one field for
             * giving back a error message. When an axception occours, the
             * client side of Axis will throw an RemoteException which includes
             * the class name of the thrown exception. There is no way to get
             * more information like the original stacktrace !!!
             */

            System.exit(1);
        } catch (MalformedURLException e) {
            System.err.println("failed (" + e.toString() + ")");
            System.exit(1);
        } catch (ServiceException e) {
            System.err.println("Service unavailable (" + e.toString() + ")");
            System.exit(1);
        } catch (IOException e) {
            System.err.println("can't read sequence file " + args[0]);
            System.exit(1);
        }
    }

    /*
     * ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ following
     * function(s) used by class
     * +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     */



    /** static method parse Inputparameter into a Hashtable */
    private static Hashtable parseParameter(String args[]) {
        Hashtable<Object, Object> prop = new Hashtable<Object, Object>();
        prop.put("MATRIX", new String());
        prop.put("GAPOPEN", new Integer(0));
        prop.put("GAPEXT", new Integer(0));
        prop.put("F", new String());
        Hashtable<Object, Object> ret = new Hashtable<Object, Object>();
        String key = "";
        for (int i = 0; i < args.length; ++i) {
            String current = args[i];

            /* found key */
            if (current.startsWith("-")) {
                /* check - maybe boolean */
                if ((key != null) && (prop.get(key) != null)) {
                    Class c = (prop.get(key)).getClass();
                    if ((c.getName()).equals("java.lang.Boolean")) {
                        ret.put(key, new Boolean(true));
                    }
                }
                /* remove -- */
                key = current.replaceAll("-", "");

            } else {
                /* found value, check if current key exists in prop */
                if (prop.get(key) != null) {

                    /* get Class of value */
                    Class c = (prop.get(key)).getClass();
                    if ((c.getName()).equals("java.lang.Integer")) {
                        ret.put(key, new Integer(Integer.parseInt(current)));
                    } else if ((c.getName()).equals("java.lang.String")) {
                        ret.put(key, current);
                    } else if ((c.getName()).equals("java.lang.Double")) {
                        ret.put(key, new Double(Double.parseDouble(current)));
                    }
                }
                key = null;
            }
        }

        return ret;
    }
    

    /** convert a Hashtable to an ObjectArray */
    private static Object[] hashtable2array(Hashtable ht) {
        Set keys = ht.keySet();
        Object ret[] = new Object[keys.size() * 2];
        int counter = 0;
        for (Iterator i = keys.iterator(); i.hasNext();) {
            Object key = i.next();
            ret[counter] = key;
            counter++;
            ret[counter] = ht.get(key);
            counter++;
        }
        return ret;
    }

}