/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 * 
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.ws.jws2;

import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.List;

import javax.swing.*;

import jalview.datamodel.*;
import jalview.gui.*;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;

/**
 * DOCUMENT ME!
 * 
 * @author $author$
 * @version $Revision$
 */
public class MsaWSClient extends Jws2Client
{
  /**
   * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
   */
  MsaWS server;

  AlignFrame alignFrame;

  private Preset preset;

  private List<Argument> paramset;

  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
          jalview.datamodel.AlignmentView msa, boolean submitGaps,
          boolean preserveOrder, Alignment seqdataset,
          AlignFrame _alignFrame)
  {
    this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
            seqdataset, _alignFrame);
    // TODO Auto-generated constructor stub
  }

  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
          String altitle, jalview.datamodel.AlignmentView msa,
          boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
          AlignFrame _alignFrame)
  {
    this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
            seqdataset, _alignFrame);
    // TODO Auto-generated constructor stub
  }

  /**
   * Creates a new MsaWSClient object that uses a service given by an externally
   * retrieved ServiceHandle
   * 
   * @param sh
   *          service handle of type AbstractName(MsaWS)
   * @param altitle
   *          DOCUMENT ME!
   * @param msa
   *          DOCUMENT ME!
   * @param submitGaps
   *          DOCUMENT ME!
   * @param preserveOrder
   *          DOCUMENT ME!
   */

  public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
          List<Argument> arguments, boolean editParams, String altitle,
          jalview.datamodel.AlignmentView msa, boolean submitGaps,
          boolean preserveOrder, Alignment seqdataset,
          AlignFrame _alignFrame)
  {
    super();
    alignFrame = _alignFrame;
    if (!(sh.service instanceof MsaWS))
    {
      // redundant at mo - but may change
      JOptionPane
              .showMessageDialog(
                      Desktop.desktop,
                      "The Service called \n"
                              + sh.serviceType
                              + "\nis not a \nMultiple Sequence Alignment Service !",
                      "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);

      return;
    }
    server = sh.service;
    this.preset = preset;
    this.paramset = arguments;
    if (editParams)
    {
      WsJobParameters jobParams = new WsJobParameters(sh, preset);
      if (!jobParams.showRunDialog())
      {
        return;
      }
      if ((this.preset = jobParams.getPreset())==null)
      {
        paramset = jobParams.getJobParams();
      } else {
        paramset = null; // no user supplied parameters.
      }
    }

    if ((wsInfo = setWebService(sh, false)) == null)
    {
      JOptionPane.showMessageDialog(Desktop.desktop,
              "The Multiple Sequence Alignment Service named "
                      + sh.serviceType + " is unknown",
              "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);

      return;
    }
    startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);

  }

  public MsaWSClient()
  {
    super();
    // add a class reference to the list
  }

  private void startMsaWSClient(String altitle, AlignmentView msa,
          boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
  {
    // if (!locateWebService())
    // {
    // return;
    // }

    wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
            + " of " + altitle + "\nJob details\n");
    String jobtitle = WebServiceName.toLowerCase();
    if (jobtitle.endsWith("alignment"))
    {
      if (submitGaps
              && (!jobtitle.endsWith("realignment") || jobtitle
                      .indexOf("profile") == -1))
      {
        int pos = jobtitle.indexOf("alignment");
        jobtitle = WebServiceName.substring(0, pos) + "re-alignment of "
                + altitle;
      }
      else
      {
        jobtitle = WebServiceName + " of " + altitle;
      }
    }
    else
    {
      jobtitle = WebServiceName + (submitGaps ? " re" : " ")
              + "alignment of " + altitle;
    }

    MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
            WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
            submitGaps, preserveOrder, seqdataset);
    wsInfo.setthisService(msathread);
    msathread.start();
  }

  protected String getServiceActionKey()
  {
    return "MsaWS";
  }

  protected String getServiceActionDescription()
  {
    return "Multiple Sequence Alignment";
  }

  /**
   * look at ourselves and work out if we are a service that can take a profile
   * and align to it
   * 
   * @return true if we can send gapped sequences to the alignment service
   */
  private boolean canSubmitGaps()
  {
    // TODO: query service or extract service handle props to check if we can
    // realign
    return (WebServiceName.indexOf("lustal") > -1); // cheat!
  }

  public void attachWSMenuEntry(JMenu rmsawsmenu,
          final Jws2Instance service, final AlignFrame alignFrame)
  {
    setWebService(service, true); // headless
    boolean finished = true, submitGaps = false;
    JMenu msawsmenu = rmsawsmenu;
    String svcname = WebServiceName;
    if (svcname.endsWith("WS"))
    {
      svcname = svcname.substring(0,svcname.length()-2);
    }
    String calcName = svcname + " ";
    if (canSubmitGaps())
    {
      msawsmenu = new JMenu(svcname);
      rmsawsmenu.add(msawsmenu);
      calcName = "";
    }

    do
    {
      if (submitGaps == true)
      {
        msawsmenu = new JMenu("profile " + svcname);
        rmsawsmenu.add(msawsmenu);
      }
      final boolean withGaps = submitGaps;
      JMenuItem method = new JMenuItem(calcName + "Defaults");
      method.setToolTipText("Align with default settings");

      method.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
          new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
                  true, alignFrame.getViewport().getAlignment()
                          .getDataset(), alignFrame);

        }
      });
      msawsmenu.add(method);
      method = new JMenuItem(calcName + "Edit and run ...");
      method.setToolTipText("View and change the parameters before alignment.");

      method.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          AlignmentView msa = alignFrame.gatherSequencesForAlignment();
          new MsaWSClient(service, null, null, true, alignFrame.getTitle(),
                  msa, withGaps, true, alignFrame.getViewport()
                          .getAlignment().getDataset(), alignFrame);

        }
      });
      msawsmenu.add(method);
      PresetManager presets = service.getPresets();
      if (presets != null && presets.getPresets().size() > 0)
      {
        JMenu presetlist = new JMenu(calcName + "Presets");

        for (final Preset preset : (List<Preset>) presets.getPresets())
        {
          final JMenuItem methodR = new JMenuItem(preset.getName());
          methodR.setToolTipText("<html><p>"+preset.getDescription()+"</p></html>");
          methodR.addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              AlignmentView msa = alignFrame.gatherSequencesForAlignment();
              new MsaWSClient(service, preset, alignFrame.getTitle(), msa,
                      false, true, alignFrame.getViewport().getAlignment()
                              .getDataset(), alignFrame);

            }

          });
          presetlist.add(methodR);
        }
        msawsmenu.add(presetlist);
      }
      if (!submitGaps && canSubmitGaps())
      {
        submitGaps = true;
        finished = false;
      }
      else
      {
        finished = true;
      }
    } while (!finished);
  }
}