package jalview.io;

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
{

  JInternalFrame outputFrame = new JInternalFrame();
  CutAndPasteTransfer output = new CutAndPasteTransfer(false);
  int jobsRunning = 0;
  ext.vamsas.JpredSoapBindingStub server;

  public JPredClient(SequenceI seq)
  {
    output.formatForOutput();
    outputFrame.setContentPane(output);

    output.setText("Job details for prediction on sequence :\nName : "
                   + seq.getName() + "\nSequence : " + seq.getSequence() + "\n");
    Desktop.addInternalFrame(outputFrame,
                             "JNet secondary structure prediction job", 800,
                             300);

    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
    try {
      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
    }
    catch (Exception ex) {
      output.setText("Serious! JPred Service location failed\nfor URL :"
                     +loc.getjpredAddress()+"\n"+ex.getMessage());
    }

    JPredThread jthread = new JPredThread(seq);
    jthread.start();
    ImageTwirler thread = new ImageTwirler();
    thread.start();
  }

  class ImageTwirler
      extends Thread
  {
    ImageIcon[] imageIcon;
    int imageIndex = 0;
    public ImageTwirler()
    {
      imageIcon = new ImageIcon[9];
      for (int i = 0; i < 9; i++)
      {
        java.net.URL url = getClass().getResource("/images/dna" + (i + 1) +
                                                  ".gif");
        if (url != null)
          imageIcon[i] = new ImageIcon(url);
      }
    }

    public void run()
    {
      while (jobsRunning > 0)
      {
        try
        {
          Thread.sleep(100);
          imageIndex++;
          imageIndex %= 9;
          outputFrame.setFrameIcon(imageIcon[imageIndex]);
          outputFrame.setTitle("JNet Secondary Structure Prediction : " +
                               jobsRunning + " jobs running.");

        }
        catch (Exception ex)
        {}

      }
    }
  }

  class JPredThread
      extends Thread
  {
    String OutputHeader;
    ext.vamsas.Secstructpred result;
    ext.vamsas.Sequence sequence;
    String jobId;
    boolean jobComplete = false;
    int allowedServerExceptions = 3; // thread dies if too many exceptions.
    JPredThread(SequenceI seq)
    {
      OutputHeader = output.getText();
      this.sequence = new ext.vamsas.Sequence();
      this.sequence.setId(seq.getName());
      this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));
    }

    public void run()
    {

      StartJob();

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

          if (result.getOutput().indexOf("Job") != 0)
          {
            parseResult();
            jobComplete = true;
            jobsRunning--;
          }
          else
          {
            output.setText(OutputHeader + "\n" + result.getOutput());
          }
          Thread.sleep(5000);
          //      System.out.println("I'm alive "+seqid+" "+jobid);

        }
        catch (Exception ex)
        {
          allowedServerExceptions--;
          String msg = output.getText();
          output.setText(msg + "\nJPredWS Server exception!\n" + ex.getMessage());
        }
      }
    }

    void StartJob()
    {
      try
      {
        jobId = server.predict(sequence);
        System.out.println(jobId);
      }
      catch (Exception e)
      {
        System.out.println("JPredWS Client: Failed to submit the prediction\n" +
                           e.toString() + "\n");
        e.printStackTrace();
      }
    }

    void parseResult()
    {
      output.setText(OutputHeader + result.getOutput());
      try {
        JPredFile prediction=new JPredFile(result.getOutput(), "Paste");
        SequenceI[] preds = prediction.getSeqsAsArray();
        int i=0;
        // Rename the query sequence
        while (i<preds.length && !preds[i].getName().equals("QUERY")) {
          i++;
        }
        if (i<preds.length) {
          preds[i].setName(sequence.getId());
        }
        AlignFrame af = new AlignFrame(new Alignment(preds));
        /*  JBPNote - need to set correct style of display for the secstrpred alignment object.
            af.clustalColour.setSelected(true);
            af.clustalColour_actionPerformed(null);
         */
        Desktop.addInternalFrame(af, "JNet Prediction for sequence "+sequence.getId(),
                                 700, 500);
      }
      catch (Exception e) {
        output.setText(output.getText()+"\nError! File did not parse correctly\n"+e.getMessage()+"\n");
        e.printStackTrace();
      }

    }

  }
}