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
    extends WSClient
{
    /**
     * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
     */
    ext.vamsas.MuscleWS server;

  private boolean setWebService(String MsaWSName) {
    if (MsaWServices.info.containsKey(MsaWSName)) {
      WebServiceName = MsaWSName;
      String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);
      WsURL = wsinfo[0];
      WebServiceJobTitle = wsinfo[1];
      WebServiceReference = wsinfo[2];
      return true;
    } else {
      return false;
    }
  }


  public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
  {
    if (setWebService(MsaWSName)==false) {
      JOptionPane.showMessageDialog(Desktop.desktop, "The Multiple Sequence Alignment Service named "+MsaWSName+" is unknown",
                                    "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
      return;
    }

    wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);

    wsInfo.setProgressText("Alignment of "+altitle+"\nJob details\n");

    // TODO: MuscleWS transmuted to generic MsaWS client
    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
    try {
      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
    }
    catch (Exception ex) {
      wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
                     +WsURL+"\n"+ex.getMessage());
      wsInfo.setStatus(wsInfo.ERROR);
      ex.printStackTrace();
    }

    MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
    wsInfo.setthisService(musclethread);
    musclethread.start();
  }


  protected class MsaWSThread extends Thread implements WSClientI
  {
    String ServiceName = WebServiceName;

    public boolean isCancellable()
    {
      return true;
    }

    String OutputHeader;
    vamsas.objects.simple.MsaResult result = null;

    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
        SequenceSet();

    Hashtable SeqNames = null;
    boolean submitGaps = false,// default is to strip gaps from sequences
        preserveOrder = true; // and always store and recover sequence order

    String jobId;
    String alTitle; // name which will be used to form new alignment window.
    int allowedServerExceptions = 3; // thread dies if too many exceptions.
    MsaWSThread(String title, SequenceI[] msa, boolean subgaps, boolean presorder)
    {
      alTitle = title;
      submitGaps = subgaps;
      preserveOrder = presorder;

      OutputHeader = wsInfo.getProgressText();
      SeqNames = new Hashtable();
      vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
          Sequence[msa.length];

      for (int i = 0; i < msa.length; i++)
      {
        String newname = jalview.analysis.SeqsetUtils.unique_name(i);
        // uniquify as we go
        // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
        SeqNames.put(newname, jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
        seqarray[i] = new vamsas.objects.simple.Sequence();
        seqarray[i].setId(newname);
        seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
                           : 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) {
          jobId=jobsubmit.getJobId();
          System.out.println(WsURL+" Job Id '"+jobId+"'");
        } else {
          throw new Exception(jobsubmit.getJobId());
        }
      }
      catch (Exception e)
      {
        System.err.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) {
          AlignmentOrder msaorder = new AlignmentOrder(seqs);

          if (preserveOrder) {
            jalview.analysis.AlignmentSorter.recoverOrder(seqs);
          }

          jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);

          Alignment al = new Alignment(seqs);

          // TODO: JBPNote Should also rename the query sequence sometime...
          AlignFrame af = new AlignFrame(al);
          af.addSortByOrderMenuItem(ServiceName+" Ordering", msaorder);

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

    }

  }
}