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.*;
import vamsas.objects.*;

public class MsaWSClient
{
  int jobsRunning = 0;
  ext.vamsas.MuscleWS server;
  WebserviceInfo wsInfo;
  /**
   * MsaWSClient
   *
   * @param msa SequenceI[]
   */
  public MsaWSClient(SequenceI[] msa)
  {
    wsInfo = new jalview.gui.WebserviceInfo("Muscle Alignment job",
                                "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.");


    wsInfo.setProgressText("Job details\n");


    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
    try {
      this.server = (MuscleWS) loc.getMuscleWS(); // JBPNote will be set from properties
    }
    catch (Exception ex) {
      wsInfo.setProgressText("Serious! MuscleWS Service location failed\nfor URL :"
                     +loc.getMuscleWSAddress()+"\n"+ex.getMessage());
      ex.printStackTrace();
    }

    MsaWSThread musclethread = new MsaWSThread(msa);
    wsInfo.setthisService(musclethread);
    musclethread.start();
  }


  protected class MsaWSThread extends Thread implements WSClientI
  {
    String ServiceName = "MuscleWS";
    public boolean isCancellable()
    {
      return true;
    }

    String OutputHeader;
    vamsas.objects.simple.MsaResult result = null;
    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
        SequenceSet();
    String jobId;
    int allowedServerExceptions = 3; // thread dies if too many exceptions.
    MsaWSThread(SequenceI[] msa)
    {
      OutputHeader = wsInfo.getProgressText();
      vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
          Sequence[msa.length];
      for (int i = 0; i < msa.length; i++)
      {
        seqarray[i] = new vamsas.objects.simple.Sequence();
        seqarray[i].setId(msa[i].getName());
        seqarray[i].setSeq(AlignSeq.extractGaps("-. ", msa[i].getSequence()));
      }
      this.seqs = new vamsas.objects.simple.SequenceSet();
      this.seqs.setSeqs(seqarray);
    }

    boolean jobComplete = false;

    public void cancelJob() {
      if (!jobComplete) {
        String cancelledMessage="";
        try {
          vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
          if (cancelledJob.getStatus() == 2)
          {
            // CANCELLED_JOB
            cancelledMessage = "Job cancelled.";
            wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
            jobComplete = true;
            jobsRunning--;
            result = null;
          }
          else
          if (cancelledJob.getStatus() == 3)
          {
            // VALID UNSTOPPABLE JOB
            cancelledMessage +=
                "Server cannot cancel this job. just close the window.\n";
          }
          if (cancelledJob.getJobId() != null)
            cancelledMessage += "[" + cancelledJob.getJobId() + "]";
          cancelledMessage +="\n";
        } catch (Exception exc) {
          cancelledMessage +="\nProblems cancelling the job : Exception received...\n"+exc+"\n";
          exc.printStackTrace();
        }
        wsInfo.setProgressText(OutputHeader + cancelledMessage+"\n");
      }
    }

    public void run()
    {

      StartJob();

      while (!jobComplete && (allowedServerExceptions > 0))
      {
        try
        {
          result = server.getResult(jobId);

         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()))
            {
              Thread.sleep(5000);
              //  System.out.println("I'm alive "+seqid+" "+jobid);
            }
          }
        }
        catch (Exception ex)
        {
          allowedServerExceptions--;
          wsInfo.appendProgressText("\n"+ServiceName+" Server exception!\n" + ex.getMessage());
          ex.printStackTrace();
        }
      }

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

    void StartJob()
    {
      try
      {
        vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
        if (jobsubmit.getStatus()==1) {
          System.out.println(jobId=jobsubmit.getJobId());
        } else {
          throw new Exception(jobsubmit.getJobId());
        }
      }
      catch (Exception e)
      {
        System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +
                           e.toString() + "\n");
        e.printStackTrace();
      }
    }

    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));
    }
    private jalview.datamodel.Sequence[] getVamsasAlignment(vamsas.objects.simple.Alignment valign) {
      vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
      jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
      for (int i=0, j=seqs.length; i<j;i++)
        msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i].getSeq());
      return msa;
    }
    void parseResult()
    {
      SequenceI[] seqs=null;
      try {
        // OutputHeader = output.getText();
        if (result.isFailed()) {
          OutputHeader +="Job failed.\n";
        }
        if (result.getStatus()!=null) {
          OutputHeader += "\n"+result.getStatus();
        }
        if (result.getMsa()!=null) {
          OutputHeader += "\nAlignment Object Method Notes\n";
          String lines[] = result.getMsa().getMethod();
          for (int line=0;line<lines.length; line++)
            OutputHeader+=lines[line]+"\n";

          // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
          seqs = getVamsasAlignment(result.getMsa());
        }

        wsInfo.setProgressText(OutputHeader);
        if (seqs!=null) {
          Alignment al;
          al = new Alignment(seqs);

          // TODO: JBPNote Should also rename the query sequence sometime...
          AlignFrame af = new AlignFrame(al);
          Desktop.addInternalFrame(af,
                                   ServiceName + " Alignment",
                                   AlignFrame.NEW_WINDOW_WIDTH,
                                   AlignFrame.NEW_WINDOW_HEIGHT);
        }
      }catch(Exception ex){ex.printStackTrace();}

    }

  }
  }