/*
* 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.ws;

import org.apache.axis.client.*;
import javax.xml.namespace.QName;
import java.util.*;
import jalview.datamodel.*;
import jalview.gui.*;
import javax.swing.*;
import java.util.*;
import java.awt.*;
import jalview.analysis.AlignSeq;
import ext.vamsas.*;

public class JPredClient
    extends WSClient
{
  ext.vamsas.JPredWS server;
  String altitle = "";
  java.util.Hashtable SequenceInfo = null;
  private WebserviceInfo setWebService()
  {
    WebServiceName = "JNetWS";
    WebServiceJobTitle = "JNet secondary structure prediction";
    WebServiceReference =
        "\"Cuff J. A and Barton G.J (1999) Application of enhanced "
        + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
        + "Proteins 40:502-511\".";
    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
                                               WebServiceReference);

    return wsInfo;
  }

    private boolean locateWebService()
    {

      JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
      try
      {
        this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
        ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
      }
      catch (Exception ex)
      {
        JOptionPane.showMessageDialog(Desktop.desktop,
            "The Secondary Structure Prediction Service named "
                                      + WebServiceName + " at " + WsURL +
                                      " couldn't be located.",
                                      "Internal Jalview Error",
                                      JOptionPane.WARNING_MESSAGE);
        wsInfo.setProgressText("Serious! " + WebServiceName +
                               " Service location failed\nfor URL :"
                               + WsURL + "\n" + ex.getMessage());
        wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
        return false;
      }
      return true;
    }

    public JPredClient(String title, SequenceI[] msf)
    {
      wsInfo = setWebService();
      SequenceI seq = msf[0];
      altitle = "JNet prediction on " + seq.getName() +
          " using alignment from " + title;

      wsInfo.setProgressText("Job details for MSA based prediction (" + title +
                             ") on sequence :\n>"
                             + seq.getName() + "\n"
                             + AlignSeq.extractGaps("-. ", seq.getSequence()) +
                             "\n");

      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
      if (!locateWebService())
        return;

      JPredThread jthread = new JPredThread(msf);
      jthread.start();
    }

    public JPredClient(String title, SequenceI seq)
    {
      wsInfo = setWebService();
      wsInfo.setProgressText("Job details for prediction on sequence :\n>"
                             + seq.getName() + "\n" +
                             AlignSeq.extractGaps("-. ", seq.getSequence()) +
                             "\n");
      altitle = "JNet prediction for sequence " + seq.getName() + " from " +
          title;

      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);

      if (!locateWebService())
              return;

      JPredThread jthread = new JPredThread(seq);
      jthread.start();
    }

    class JPredThread
        extends Thread
    {
      String OutputHeader;
      ext.vamsas.JpredResult result;
      ext.vamsas.Sequence sequence;
      ext.vamsas.Msfalignment msa;
      String jobId;
      boolean jobComplete = false;
      int allowedServerExceptions = 3; // thread dies if too many exceptions.
      JPredThread(SequenceI seq)
      {
        OutputHeader = wsInfo.getProgressText();
        this.sequence = new ext.vamsas.Sequence();
        this.sequence.setId(seq.getName());
        this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
      }

      JPredThread(SequenceI[] msf)
      {
        OutputHeader = wsInfo.getProgressText();
        this.sequence = new ext.vamsas.Sequence();
        this.sequence.setId(msf[0].getName());
        this.sequence.setSeq(AlignSeq.extractGaps("-. ", msf[0].getSequence()));
        jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
        this.msa = new ext.vamsas.Msfalignment();
        msa.setMsf(mwrite.print(msf));
      }

      public void run()
      {

        StartJob();

        while (!jobComplete && (allowedServerExceptions > 0))
        {
          try
          {
            if ( (result = server.getresult(jobId)) == null)
            {
              throw (new Exception(
                  "Timed out when communicating with server\nTry again later.\n"));
            }

            if (result.isRunning())
            {
              wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
            }
            else if (result.isQueued())
            {
              wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
            }

            if (result.isFinished())
            {
              parseResult();
              jobComplete = true;
              jobsRunning--;
            }
            else
            {
              wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
              if (! (result.isJobFailed() || result.isServerError()))
              {
                try
                {
                  Thread.sleep(5000);
                }
                catch (InterruptedException ex1)
                {
                }
                //  System.out.println("I'm alive "+seqid+" "+jobid);
              }
              else
              {
                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
              }
            }
          }
          catch (Exception ex)
          {
            allowedServerExceptions--;
            wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
                                      ex.getMessage());
            try
            {
              if (allowedServerExceptions > 0)
              {
                Thread.sleep(5000);
              }
            }
            catch (InterruptedException ex1)
            {
            }
          }
        }

        if (! (result.isJobFailed() || result.isServerError()))
        {
          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
        }
        else
        {
          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
        }
      }

      void StartJob()
      {
        try
        {
          if (msa != null)
          {
            jobId = server.predictOnMsa(msa);
          }
          else
          {
            jobId = server.predict(sequence);
          }
          if (jobId != null)
          {
            if (jobId.startsWith("Broken"))
            {
              throw new Exception("Submission " + jobId);
            }
            else
            {
              System.out.println(WsURL + " Job Id '" + jobId + "'");
            }
          }
          else
          {
            throw new Exception("Server timed out - try again later\n");

          }
        }
        catch (Exception e)
        {
          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
          allowedServerExceptions = 0;
          jobComplete = false;
          wsInfo.appendProgressText("Failed to submit the prediction: " +
                                    e.toString() + "\nJust close the window\n");
          System.err.println(
              "JPredWS Client: Failed to submit the prediction\n" +
              e.toString() + "\n");
          // e.printStackTrace(); TODO: JBPNote DEBUG
        }
      }

      private void addFloatAnnotations(Alignment al, int[] gapmap,
                                       Vector values, String Symname,
                                       String Visname, float min, float max,
                                       int winLength)
      {

        Annotation[] annotations = new Annotation[al.getWidth()];
        for (int j = 0; j < values.size(); j++)
        {
          float value = Float.parseFloat(values.get(j).toString());
          annotations[gapmap[j]] = new Annotation("", value + "", ' ', value);
        }
        al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations,
                                                 min, max, winLength));
      }

      void parseResult()
      {
        // OutputHeader = output.getText();
        if (result.isFailed())
        {
          OutputHeader += "Job failed.\n";
        }
        if (result.getStatus() != null)
        {
          OutputHeader += "\n" + result.getStatus();
        }
        if (result.getPredfile() != null)
        {
          OutputHeader += "\n" + result.getPredfile();
          // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
        }
        if (result.getAligfile() != null)
        {
          OutputHeader += "\n" + result.getAligfile();
        }
        wsInfo.setProgressText(OutputHeader);
        try
        {
          // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
          jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
              getPredfile(), "Paste");
          SequenceI[] preds = prediction.getSeqsAsArray();
          Alignment al;
          int FirstSeq; // the position of the query sequence in Alignment al
          boolean noMsa = true; // set if no MSA has been returned by JPred

          if (this.msa != null && result.getAligfile() != null)
          {
            // we ignore the returned alignment if we only predicted on a single sequence
            String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
                "Paste");
            if (jalview.io.FormatAdapter.formats.contains(format))
            {
              al = new Alignment(jalview.io.FormatAdapter.readFile(result.
                  getAligfile(), "Paste", format));
              noMsa = false;
              FirstSeq = 0;
            }
            else
            {
              throw (new Exception("Unknown format 'format' for file : \n" +
                                   result.getAligfile()));
            }

          }
          else
          {
            al = new Alignment(preds);
            FirstSeq = prediction.getQuerySeqPosition();
          }

          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(
              FirstSeq), SequenceInfo))
          {
            throw (new Exception(
                "Couldn't recover sequence properties for JNet Query sequence!"));
          }

          AlignmentAnnotation annot;
          Annotation[] annotations = null;
          int i = 0;
          int width = preds[0].getSequence().length();

          int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();

          if (gapmap.length != width)
          {
            throw (new Exception(
                "Jnet Client Error\nNumber of residues in supposed query sequence :\n"
                + al.getSequenceAt(FirstSeq).getName() + "\n"
                + al.getSequenceAt(FirstSeq).getSequence()
                + "\nDiffer from number of prediction sites in \n" +
                result.getPredfile() + "\n"));
          }
          // JBPNote Should also rename the query sequence sometime...
          i = 0;
          while (i < preds.length)
          {
            String id = preds[i].getName().toUpperCase();
            if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
                id.startsWith("JPRED"))
            {
              annotations = new Annotation[al.getWidth()];

              if (id.equals("JNETPRED")
                  || id.equals("JNETPSSM")
                  || id.equals("JNETFREQ")
                  || id.equals("JNETHMM")
                  || id.equals("JNETALIGN")
                  || id.equals("JPRED"))
              {
                for (int j = 0; j < width; j++)
                {
                  annotations[gapmap[j]] = new Annotation("", "",
                      preds[i].getCharAt(j), 0);
                }
              }
              else if (id.equals("JNETCONF"))
              {
                for (int j = 0; j < width; j++)
                {
                  float value = Float.parseFloat(preds[i].getCharAt(j) + "");
                  annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +
                      "", "", preds[i].getCharAt(j), value);
                }
              }
              else
              {
                for (int j = 0; j < width; j++)
                {
                  annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +
                      "", "", ' ', 0);
                }
              }

              if (id.equals("JNETCONF"))
              {
                annot = new AlignmentAnnotation(preds[i].getName(),
                                                "JNet Output",
                                                annotations, 0f, 10f, 1);
              }

              else
              {
                annot = new AlignmentAnnotation(preds[i].getName(),
                                                "JNet Output",
                                                annotations);
              }
              al.addAnnotation(annot);
              if (noMsa)
              {
                al.deleteSequence(preds[i]);
              }
            }
            i++;
          }

          Hashtable scores = prediction.getScores();
          /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
                                "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);

            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
           "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);

            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
                                "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
           */
          AlignFrame af = new AlignFrame(al);

          Desktop.addInternalFrame(af,
                                   altitle,
                                   AlignFrame.NEW_WINDOW_WIDTH,
                                   AlignFrame.NEW_WINDOW_HEIGHT);
        }
        catch (Exception ex)
        {
          ex.printStackTrace();
        }

      }

    }
  }