package jalview.ws;

import java.util.*;

import jalview.analysis.*;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.datamodel.Alignment;
import jalview.gui.*;
import jalview.io.*;
import jalview.util.*;
import vamsas.objects.simple.JpredResult;

class JPredThread
    extends WSThread implements WSClientI
{
  // TODO: put mapping between JPredJob input and input data here - JNetAnnotation adding is done after result parsing.
  class JPredJob
      extends WSThread.WSJob
  {
    // TODO: make JPredJob deal only with what was sent to and received from a JNet service
    int[] predMap = null; // mapping from sequence(i) to the original sequence(predMap[i]) being predicted on
    vamsas.objects.simple.Sequence sequence;
    vamsas.objects.simple.Msfalignment msa;
    java.util.Hashtable SequenceInfo = null;
    int msaIndex = 0; // the position of the original sequence in the array of Sequences in the input object that this job holds a prediction for
    /**
     *
     * @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;
    }

    /**
     *
     * @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.
     * @throws Exception
     */
    public Object[] getResultSet()
        throws Exception
    {
      if (result == null || !result.isFinished())
      {
        return null;
      }
      Alignment al = null;
      ColumnSelection alcsel = 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))
        {
          SequenceI sqs[];
          if (predMap != null)
          {
            Object[] alandcolsel = input.getAlignmentAndColumnSelection(
                alignFrame.getViewport().getGapCharacter());
            sqs = (SequenceI[]) alandcolsel[0];
            al = new Alignment(sqs);
            alcsel = (ColumnSelection) alandcolsel[1];
          }
          else
          {
            al = new FormatAdapter().readFile(result.getAligfile(),
                                              "Paste", format);
            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, predMap);

        }
        else
        {
          throw (new Exception(
              "Unknown format " + format + " for file : \n" +
              result.getAligfile()));
        }
      }
      else
      {
        al = new Alignment(preds);
        FirstSeq = prediction.getQuerySeqPosition();
        if (predMap != null)
        {
          char gc = alignFrame.getViewport().getGapCharacter();
          SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.
                                           getAlignmentAndColumnSelection(gc))[
              0];
          if (this.msaIndex >= sqs.length)
          {
            throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
          }

          /////
          //Uses RemoveGapsCommand
          /////
          new jalview.commands.RemoveGapsCommand("Remove Gaps",
                                                 new SequenceI[]
                                                 {sqs[msaIndex]},
                                                 alignFrame.getCurrentView().
                                                 getAlignment());

          SequenceI profileseq = al.getSequenceAt(FirstSeq);
          profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
        }

        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, predMap);
          SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
          alignToProfileSeq(al, profileseq);
          if (predMap != null)
          {
            // Adjust input view for gaps
            // propagate insertions into profile
            alcsel = propagateInsertions(profileseq, al, input);
          }
        }
      }
      return new Object[]
          {
          al, alcsel}; // , FirstSeq, noMsa};
    }

    /**
     * Given an alignment where all other sequences except profileseq are aligned to the ungapped profileseq, insert gaps in the other sequences to realign them with the residues in profileseq
     * @param al
     * @param profileseq
     */
    private void alignToProfileSeq(Alignment al, SequenceI profileseq)
    {
      char gc = al.getGapCharacter();
      int[] gapMap = profileseq.gapMap();
      // insert gaps into profile
      for (int lp = 0, r = 0; r < gapMap.length; r++)
      {
        if (gapMap[r] - lp > 1)
        {
          StringBuffer sb = new StringBuffer();
          for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
          {
            sb.append(gc);
          }
          for (int s = 1, ns = al.getHeight(); s < ns; s++)
          {
            String sq = al.getSequenceAt(s).getSequenceAsString();
            int diff = gapMap[r] - sq.length();
            if (diff > 0)
            {
              // pad gaps
              sq = sq + sb;
              while ( (diff = gapMap[r] - sq.length()) > 0)
              {
                sq = sq +
                    ( (diff >= sb.length()) ? sb.toString() :
                     sb.substring(0, diff));
              }
              al.getSequenceAt(s).setSequence(sq);
            }
            else
            {
              al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r]) +
                                              sb.toString() +
                                              sq.substring(gapMap[r]));
            }
          }
        }
        lp = gapMap[r];
      }
    }

    /**
     * Add gaps into the sequences aligned to profileseq under the given AlignmentView
     * @param profileseq
     * @param al
     * @param input
     */
    private ColumnSelection propagateInsertions(SequenceI profileseq,
                                                Alignment al,
                                                AlignmentView input)
    {
      char gc = al.getGapCharacter();
      Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
      ColumnSelection nview = (ColumnSelection) alandcolsel[1];
      SequenceI origseq;
      nview.pruneDeletions(ShiftList.parseMap( (origseq = ( (SequenceI[])
          alandcolsel[0])[0]).gapMap())); // recover original prediction sequence's mapping to view.
      int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());
      int spos = 0;
      int offset = 0;
      //  input.pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()))
      // add profile to visible contigs
      for (int v = 0; v < viscontigs.length; v += 2)
      {
        if (viscontigs[v] > spos)
        {
          StringBuffer sb = new StringBuffer();
          for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
          {
            sb.append(gc);
          }
          for (int s = 0, ns = al.getHeight(); s < ns; s++)
          {
            SequenceI sqobj = al.getSequenceAt(s);
            if (sqobj != profileseq)
            {
              String sq = al.getSequenceAt(s).getSequenceAsString();
              if (sq.length() <= spos + offset)
              {
                // pad sequence
                int diff = spos + offset - sq.length() - 1;
                if (diff > 0)
                {
                  // pad gaps
                  sq = sq + sb;
                  while ( (diff = spos + offset - sq.length() - 1) > 0)
                  {
                    sq = sq +
                        ( (diff >= sb.length()) ? sb.toString() :
                         sb.substring(0, diff));
                  }
                }
                sq += sb.toString();
              }
              else
              {
                al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset) +
                                                sb.toString() +
                                                sq.substring(spos + offset));
              }
            }
          }
          //offset+=sb.length();
        }
        spos = viscontigs[v + 1] + 1;
      }
      if ( (offset + spos) < profileseq.getLength())
      {
        StringBuffer sb = new StringBuffer();
        for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
        {
          sb.append(gc);
        }
        for (int s = 1, ns = al.getHeight(); s < ns; s++)
        {
          String sq = al.getSequenceAt(s).getSequenceAsString();
          // pad sequence
          int diff = origseq.getLength() - sq.length();
          while (diff > 0)
          {
            sq = sq +
                ( (diff >= sb.length()) ? sb.toString() : sb.substring(0, diff));
            diff = origseq.getLength() - sq.length();
          }
        }
      }
      return nview;
    }

    public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
    {
      super();
      this.predMap = delMap;
      String sq = AlignSeq.extractGaps(Comparison.GapChars,
                                       seq.getSequenceAsString());
      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, int[] delMap)
    {
      this(SequenceInfo, msf[0], delMap);
      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,
              String wsurl, AlignmentView alview, AlignFrame alframe)
  {
    super();
    this.altitle = altitle;
    this.server = server;
    this.wsInfo = wsinfo;
    this.input = alview;
    this.alignFrame = alframe;
    WsUrl = wsurl;
  }

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

  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;
    }
  }

  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)
    {
      Object[] res = null;
      boolean msa = false;
      for (int jn = 0; jn < jobs.length; jn++)
      {
        Object[] 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)
          {
            if (res[1] != null)
            {
              af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],
                                  AlignFrame.DEFAULT_WIDTH,
                                  AlignFrame.DEFAULT_HEIGHT);
            }
            else
            {
              af = new AlignFrame( (Alignment) res[0], AlignFrame.DEFAULT_WIDTH,
                                  AlignFrame.DEFAULT_HEIGHT);
            }
          }
          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!");
              }
                         }
                         if (!msa) {
              // update hidden regions to account for loss of gaps in profile. - if any
              // gapMap returns insert list, interpreted as delete list by pruneDeletions
              //((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
                         }*/

            af = new AlignFrame( (Alignment) res[0], (ColumnSelection) res[1],
                                AlignFrame.DEFAULT_WIDTH,
                                AlignFrame.DEFAULT_HEIGHT);
          }
          Desktop.addInternalFrame(af, altitle,
                                   AlignFrame.DEFAULT_WIDTH,
                                   AlignFrame.DEFAULT_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;
  }

}