/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package jalview.io;

import jalview.datamodel.*;

import jalview.gui.*;

import org.apache.axis.client.*;

import java.awt.*;

import java.util.*;

import javax.swing.*;

import javax.xml.namespace.QName;


public class WSWUBlastClient {
    CutAndPasteTransfer output = new CutAndPasteTransfer();
    int jobsRunning = 0;

    public WSWUBlastClient(AlignmentI al, ArrayList ids) {
        output.setText(
            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +
            "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
        Desktop.addInternalFrame(output,
            "BLASTing for unidentified sequences ", 800, 300);

        for (int i = 0; i < ids.size(); i++) {
            SequenceI sequence = al.findName(ids.get(i).toString());
            StringBuffer nonGapped = new StringBuffer();

            for (int n = 0; n < sequence.getSequence().length(); n++) {
                if (!jalview.util.Comparison.isGap(sequence.getCharAt(n))) {
                    nonGapped.append(sequence.getCharAt(n));
                }
            }

            BlastThread thread = new BlastThread(ids.get(i).toString(),
                    nonGapped.toString());
            thread.start();
            jobsRunning++;
        }

        ImageTwirler thread = new ImageTwirler();
        thread.start();
    }

    void parseResult(String id1, String res) {
        StringTokenizer st = new StringTokenizer(res, "\n");
        String data;
        String id2;
        int maxFound = 90;
        StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");

        while (st.hasMoreTokens()) {
            data = st.nextToken();

            if (data.indexOf("database=\"uniprot\" id=") > -1) {
                int index = data.indexOf("database=\"uniprot\" id=") + 23;
                id2 = data.substring(index, data.indexOf("\"", index));

                while (data.indexOf("</alignment>") == -1) {
                    data = st.nextToken();

                    if (data.indexOf("<identity>") > -1) {
                        int value = Integer.parseInt(data.substring(data.indexOf(
                                        "<identity>") + 10,
                                    data.indexOf("</identity>")));

                        if (value >= maxFound) {
                            maxFound = value;
                            buffer.append(" " + id2 + " " + value + "%; ");
                        }
                    }
                }
            }
        }

        output.setText(output.getText() + buffer.toString());
    }

    class ImageTwirler extends Thread {
        ImageIcon[] imageIcon;
        int imageIndex = 0;

        public ImageTwirler() {
            imageIcon = new ImageIcon[9];

            for (int i = 0; i < 9; i++) {
                java.net.URL url = getClass().getResource("/images/dna" +
                        (i + 1) + ".gif");

                if (url != null) {
                    imageIcon[i] = new ImageIcon(url);
                }
            }
        }

        public void run() {
            while (jobsRunning > 0) {
                try {
                    Thread.sleep(100);
                    imageIndex++;
                    imageIndex %= 9;
                    output.setFrameIcon(imageIcon[imageIndex]);
                    output.setTitle("BLASTing for unidentified sequences - " +
                        jobsRunning + " jobs running.");
                } catch (Exception ex) {
                }
            }
        }
    }

    class BlastThread extends Thread {
        String sequence;
        String seqid;
        String jobid;
        boolean jobComplete = false;

        BlastThread(String id, String sequence) {
            this.sequence = sequence;
            seqid = id;
        }

        public void run() {
            StartJob();

            while (!jobComplete) {
                try {
                    Call call = (Call) new Service().createCall();
                    call.setTargetEndpointAddress(new java.net.URL(
                            "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
                    call.setOperationName(new QName("WSWUBlast", "polljob"));

                    String result = (String) call.invoke(new Object[] {
                                jobid, "xml"
                            });

                    if ((result.indexOf("JOB PENDING") == -1) &&
                            (result.indexOf("JOB RUNNING") == -1)) {
                        parseResult(seqid, result);
                        jobComplete = true;
                        jobsRunning--;
                    }

                    Thread.sleep(5000);

                    // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
                } catch (Exception ex) {
                }
            }
        }

        void StartJob() {
            HashMap params = new HashMap();
            params.put("database", "uniprot");
            params.put("sensitivity", "low");
            params.put("sort", "totalscore");
            params.put("matrix", "pam10");
            params.put("program", "blastp");
            params.put("alignments", "5");
            params.put("outformat", "xml");
            params.put("searchtype", "1");

            byte[] seqbytes = sequence.getBytes();

            try {
                Call call = (Call) new Service().createCall();
                call.setTargetEndpointAddress(new java.net.URL(
                        "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
                call.setOperationName(new QName("WSWUBlast", "doWUBlast"));

                String result = (String) call.invoke(new Object[] {
                            params, seqbytes
                        });
                jobid = result;
                System.out.println(
                    "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +
                    jobid + "'");
            } catch (Exception exp) {
                System.err.println("WSWUBlastClient error:\n" + exp.toString());
                exp.printStackTrace();
            }
        }
    }
}