/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 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 java.util.*;

import javax.swing.*;

import ext.vamsas.*;
import jalview.analysis.*;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentView;
import jalview.gui.*;
import jalview.io.*;
import jalview.util.*;
import jalview.ws.WSThread.*;
import vamsas.objects.simple.*;

public class JPredClient
    extends WSClient
{
    /**
     * crate a new GUI JPred Job
     * @param sh ServiceHandle
     * @param title String
     * @param msa boolean - true - submit alignment as a sequence profile
     * @param alview AlignmentView
     */
    public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {
    super();
    wsInfo=setWebService(sh);
    startJPredClient(title, msa, alview, parentFrame);

  }
  /**
   * startJPredClient
   * TODO: refine submission to cope with local prediction of visible regions or multiple single sequence jobs
   * TODO: sequence representative support - could submit alignment of representatives as msa.
   * TODO:  msa hidden region prediction - submit each chunk for prediction. concatenate results of each.
   * TODO:  single seq prediction - submit each contig of each sequence for prediction (but must cope with flanking regions and short seqs)
   * @param title String
   * @param msa boolean
   * @param alview AlignmentView
   */
  private void startJPredClient(String title, boolean msa,
                                jalview.datamodel.AlignmentView alview, AlignFrame parentFrame)
  {
    AlignmentView input = alview;
    if (wsInfo == null)
    {
      wsInfo = setWebService();
    }
    Jpred server = locateWebService();
    if (server == null)
    {
      Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
      return;
    }

    SeqCigar[] msf = input.getSequences();
    SequenceI seq = msf[0].getSeq('-');
    if (msa && msf.length > 1)
    {

      String 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");
      SequenceI aln[] = new SequenceI[msf.length];
      for (int i = 0, j = msf.length; i < j; i++)
      {
        aln[i] = msf[i].getSeq('-');
      }

      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);

      JPredThread jthread = new JPredThread(wsInfo, altitle, server,
                                            SequenceInfo, aln, alview, parentFrame);
      wsInfo.setthisService(jthread);
      jthread.start();
    }
    else
    {
      if (!msa && msf.length>1)
        throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
      wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
                             seq.getName() + "\n" +
                             AlignSeq.extractGaps("-. ", seq.getSequence()) +
                             "\n");
      String altitle = "JNet prediction for sequence " + seq.getName() +
          " from " +
          title;

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

      JPredThread jthread = new JPredThread(wsInfo, altitle, server,
                                            SequenceInfo, seq, alview, parentFrame);
      wsInfo.setthisService(jthread);
      jthread.start();
    }
  }
  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)
  {
    super();
    wsInfo = setWebService(sh);
    startJPredClient(title, seq, parentFrame);
  }

  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)
  {
    wsInfo = setWebService(sh);
    startJPredClient(title, msa, parentFrame);
  }

  public JPredClient(String title, SequenceI[] msf)
  {
    startJPredClient(title, msf, null);
  }

  public JPredClient(String title, SequenceI seq)
  {
    startJPredClient(title, seq, null);
  }

  private void startJPredClient(String title, SequenceI[] msf, AlignFrame parentFrame)
  {
    if (wsInfo == null)
    {
      wsInfo = setWebService();
    }

    SequenceI seq = msf[0];

    String 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");
    SequenceI aln[] = new SequenceI[msf.length];
    for (int i = 0, j = msf.length; i < j; i++)
    {
      aln[i] = new jalview.datamodel.Sequence(msf[i]);
    }

    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);

    Jpred server = locateWebService();
    if (server==null)
    {
      return;
    }

    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, parentFrame);
    wsInfo.setthisService(jthread);
    jthread.start();
  }

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

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

    Jpred server = locateWebService();
    if (server==null)
    {
      return;
    }

    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq,null, parentFrame);
    wsInfo.setthisService(jthread);
    jthread.start();
  }

  private WebserviceInfo setWebService()
  {
    WebServiceName = "JNetWS";
    WebServiceJobTitle = "JNet secondary structure prediction";
    WebServiceReference =
        "\"Cuff J. A and Barton G.J (2000) Application of " +
        "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 ext.vamsas.Jpred locateWebService()
  {
    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
    ext.vamsas.Jpred server=null;
    try
    {
      server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
      ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub
      //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);

    }
    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(WebserviceInfo.STATE_STOPPED_SERVERERROR);

    }

    return server;
  }

  class JPredThread
      extends WSThread
      implements WSClientI
  {
    class JPredJob
        extends WSThread.WSJob
    {

      vamsas.objects.simple.Sequence sequence;
      vamsas.objects.simple.Msfalignment msa;
      java.util.Hashtable SequenceInfo = null;
      /**
       *
       * @return true if getResultSet will return a valid alignment and prediction result.
       */
      public boolean hasResults()
      {
        if (subjobComplete && result != null && result.isFinished()
            && ( (JpredResult) result).getPredfile() != null &&
            ( (JpredResult) result).getAligfile() != null)
        {
          return true;
        }
        return false;
      }

      boolean hasValidInput()
      {
        if (sequence != null)
        {
          return true;
        }
        return false;
      }

      public Alignment getResultSet()
          throws Exception
      {
        if (result == null || !result.isFinished())
        {
          return null;
        }
        Alignment al = null;
        int FirstSeq = -1; // the position of the query sequence in Alignment al

        JpredResult result = (JpredResult)this.result;

        jalview.bin.Cache.log.debug("Parsing output from JNet job.");
        // 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();
        jalview.bin.Cache.log.debug("Got prediction profile.");

        if ( (this.msa != null) && (result.getAligfile() != null))
        {
          jalview.bin.Cache.log.debug("Getting associated alignment.");
          // we ignore the returned alignment if we only predicted on a single sequence
          String format = new jalview.io.IdentifyFile().Identify(result.
              getAligfile(),
              "Paste");

          if (jalview.io.FormatAdapter.isValidFormat(format))
          {
            al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),
                "Paste", format));
            SequenceI sqs[] = new SequenceI[al.getHeight()];
            for (int i = 0, j = al.getHeight(); i < j; i++)
            {
              sqs[i] = al.getSequenceAt(i);
            }
            if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
                SequenceInfo, sqs))
            {
              throw (new Exception(
                  "Couldn't recover sequence properties for alignment."));
            }

            FirstSeq = 0;
            al.setDataset(null);

            jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
                                                          false);

          }
          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!"));
          } else {
            al.setDataset(null);
            jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
                true);
          }
        }

        return al; // , FirstSeq, noMsa};
      }
      public JPredJob(Hashtable SequenceInfo, SequenceI seq)
      {
        super();
        String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
        if (sq.length() >= 20)
        {
          this.SequenceInfo = SequenceInfo;
          sequence = new vamsas.objects.simple.Sequence();
          sequence.setId(seq.getName());
          sequence.setSeq(sq);
        }
      }

      public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
      {
        this(SequenceInfo, msf[0]);
        if (sequence != null)
        {
          if (msf.length > 1)
          {
            msa = new vamsas.objects.simple.Msfalignment();
            jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
            msa.setMsf(pileup.print(msf));
          }
        }
      }
    }
    ext.vamsas.Jpred server;
    String altitle = "";
    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, AlignmentView alview, AlignFrame alframe) {
      this.altitle = altitle;
      this.server = server;
      this.wsInfo = wsinfo;
      this.input = alview;
      this.alignFrame = alframe;
    }

//    String OutputHeader;
//    vamsas.objects.simple.JpredResult result;

    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq, AlignmentView alview, AlignFrame alframe)
    {
      this(wsinfo, altitle, server,alview, alframe);
      JPredJob job = new JPredJob(SequenceInfo, seq);
      if (job.hasValidInput())
      {
        OutputHeader = wsInfo.getProgressText();
        jobs = new WSJob[]
            {
            job};
        job.jobnum = 0;
      }
    }

    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf, AlignmentView alview, AlignFrame alframe)
    {
      this(wsinfo, altitle, server,alview, alframe);
      JPredJob job = new JPredJob(SequenceInfo, msf);
      if (job.hasValidInput())
      {
        jobs = new WSJob[]
            {
            job};
        OutputHeader = wsInfo.getProgressText();
        job.jobnum = 0;
      }
    }

    /*
        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.getState()==0)
                jalview.bin.Cache.log.debug("Finished "+jobId);
              if (result.isRunning())
              {
                wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
              }
              if (result.isQueued())
              {
                wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
              }

              wsInfo.setProgressText(OutputHeader + "\n" +
                                     result.getStatus());

              if (result.isFinished())
              {

                parseResult();
                jobComplete = true;
                jobsRunning--;
              } else {
                // catch exceptions
                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);
                  jobsRunning--;
                  jobComplete = true;
                }
              }
            }
            catch (Exception ex)
            {
              allowedServerExceptions--;

              wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
                                        ex.getMessage());

              try
              {
                if (allowedServerExceptions > 0)
                {
                  Thread.sleep(5000);
                }
              }
              catch (InterruptedException ex1)
              {
              }
            }
            catch (OutOfMemoryError er)
            {
              jobComplete = true;
              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
              JOptionPane.showInternalMessageDialog(Desktop.desktop,
     "Out of memory handling result!!"
                                                    +
     "\nSee help files for increasing Java Virtual Machine memory."
                                                    , "Out of memory",
     JOptionPane.WARNING_MESSAGE);
              System.out.println("JPredClient: "+er);
              System.gc();
            }
          }
          if (result!=null)
            if (! (result.isJobFailed() || result.isServerError()))
            {
              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
            }
            else
            {
              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
            }
        }
     */
    void StartJob(WSJob j)
    {
      if (! (j instanceof JPredJob))
      {
        throw new Error("Implementation error - StartJob(JpredJob) called on " +
                        j.getClass());
      }
      try
      {
        JPredJob job = (JPredJob) j;
        if (job.msa != null)
        {
          job.jobId = server.predictOnMsa(job.msa);
        }
        else
          if (job.sequence!=null)
          {
            job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
          }

        if (job.jobId != null)
        {
          if (job.jobId.startsWith("Broken"))
          {
            job.result = (vamsas.objects.simple.Result)new JpredResult();
            job.result.setInvalid(true);
            job.result.setStatus("Submission " + job.jobId);
          }
          else
          {
            job.submitted = true;
            job.subjobComplete = false;
            Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");
          }
        }
        else
        {
          throw new Exception("Server timed out - try again later\n");
        }
      }
      catch (Exception e)
      {
        if (e.getMessage().indexOf("Exception") > -1)
        {
          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
          wsInfo.setProgressText(j.jobnum,
                                 "Failed to submit the prediction. (Just close the window)\n"
                                 +
                                 "It is most likely that there is a problem with the server.\n");
          System.err.println(
              "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
              e.getMessage() + "\n");

          jalview.bin.Cache.log.warn("Server Exception", e);
        }
        else
        {
          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
          // JBPNote - this could be a popup informing the user of the problem.
          wsInfo.appendProgressText(j.jobnum,
                                    "Failed to submit the prediction:\n"
                                    + e.getMessage() +
                                    wsInfo.getProgressText());

          jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);

        }
        j.allowedServerExceptions = -1;
        j.subjobComplete = true;
      }
    }

    /*  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()
    {
      int results = 0; // number of result sets received
      JobStateSummary finalState = new JobStateSummary();
      try
      {
        for (int j = 0; j < jobs.length; j++)
        {
          finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
          if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
          {
            results++;
          }
        }
      }
      catch (Exception ex)
      {

        Cache.log.error("Unexpected exception when processing results for " +
                        altitle, ex);
        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
      }
      if (results > 0)
      {
        wsInfo.showResultsNewFrame
            .addActionListener(new java.awt.event.ActionListener()
        {
          public void actionPerformed(
              java.awt.event.ActionEvent evt)
          {
            displayResults(true);
          }
        });
        wsInfo.mergeResults
            .addActionListener(new java.awt.event.ActionListener()
        {
          public void actionPerformed(
              java.awt.event.ActionEvent evt)
          {
            displayResults(false);
          }
        });
        wsInfo.setResultsReady();
      }
      else
      {
        wsInfo.setFinishedNoResults();
      }
    }

    void displayResults(boolean newWindow)
    {
      // TODO: cope with multiple subjobs.
      if (jobs != null)
      {
        Alignment res = null;
        boolean msa=false;
        for (int jn = 0; jn < jobs.length; jn++)
        {
          Alignment jobres = null;
          JPredJob j = (JPredJob) jobs[jn];

          if (j.hasResults())
          {
            // hack - we only deal with all single seuqence predictions or all profile predictions
            msa = (j.msa!=null) ? true : msa;
            try
            {
              jalview.bin.Cache.log.debug("Parsing output of job " + jn);
              jobres = j.getResultSet();
              jalview.bin.Cache.log.debug("Finished parsing output.");
              if (jobs.length==1)
                res = jobres;
              else {
                  // do merge with other job results
                  throw new Error("Multiple JNet subjob merging not yet implemented.");
              }
            }
            catch (Exception e)
            {
              jalview.bin.Cache.log.error(
                  "JNet Client: JPred Annotation Parse Error",
                  e);
              wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
              wsInfo.appendProgressText(j.jobnum,
                                        OutputHeader + "\n" +
                                        j.result.getStatus() +
                                        "\nInvalid JNet job result data!\n" +
                                        e.getMessage());
              j.result.setBroken(true);
            }
          }
        }

        if (res != null)
        {
          if (newWindow)
          {
            AlignFrame af;
           if (input==null) {
             af = new AlignFrame(res);
           } else {
             java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());

             if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
               if (msa) {
                 throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
               } else {
                 // test this.
                 ((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));//gapMap returns insert list, interpreted as delete list by pruneDeletions
               }
             }
             af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]);
           }
            Desktop.addInternalFrame(af, altitle,
                                     AlignFrame.NEW_WINDOW_WIDTH,
                                     AlignFrame.NEW_WINDOW_HEIGHT);
          }
          else
          {
            Cache.log.info("Append results onto existing alignment.");
          }
        }
      }
    }
    void pollJob(WSJob job)
        throws Exception
    {
      job.result = server.getresult(job.jobId);
    }
    public boolean isCancellable()
    {
      return false;
    }

    public void cancelJob()
    {
      throw new Error("Implementation error!");
    }

    public boolean canMergeResults()
    {
      return false;
    }

  }
}