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 void 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";
  }
  public JPredClient(String title, SequenceI[] msf)
  {
    wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);
    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);

    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
    // JBPNote url will be set from properties
    try {
      this.server = loc.getjpred(new java.net.URL(WsURL));
    }
    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());
    }

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

  public JPredClient(String title, SequenceI seq)
  {
    setWebService();
    wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);
    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);

    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
    try {
      this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
    }
    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());
    }

    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.MSFfile mwrite = new jalview.io.MSFfile();
      this.msa = new ext.vamsas.Msfalignment();
      msa.setMsf(mwrite.print(msf));
    }


    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);
            } else {
              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
            }
          }
        }
        catch (Exception ex)
        {
          allowedServerExceptions--;
          wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());
        }
      }

      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);
        }
        System.out.println(WsURL+" Job Id '"+jobId+"'");
      }
      catch (Exception e)
      {
        System.err.println("JPredWS 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));
    }

    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();}

    }

  }
}